satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of human phosphodiesterase 10 in complex with 2,3-dichloro-N-(2-phenyl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyridine-4-carboxamide (PDB entry 5SJ2)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1759
R free: 0.2182
Average B factor: 38.622
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.65
Solvent content (%): 53.59
Ligand: 2,3-dichloro-N-[(4S)-2-phenyl[1,2,4]triazolo[1,5-a]pyridin-7-yl]pyridine-4-carboxamide (JWR)
Ligand formula: C18 H11 Cl2 N5 O
Ligand molecular weight: 384.219
Ligand SMILES: c1ccc(cc1)c2nc3cc(ccn3n2)NC(=O)c4ccnc(c4Cl)Cl
Ligand InChI: InChI=1S/C18H11Cl2N5O/c19-15-13(6-8-21-16(15)20)18(26)22-12-7-9-25-14(10-12)23-17(24-25)11-4-2-1-3-5-11/h1-10H,(H,22,26)
Release date: 2022-10-12
human PDE10A in complex with 1-(4-Chloro-phenyl)-3-methyl-1H-thieno[2,3-c]pyrazole-5-carboxylic acid (tetrahydro-furan-2-ylmethyl)-amide at 2.2A (PDB entry 5EDE)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 316 residues
Sequence: AQGLMQFTLPVRLCREIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1835
R free: 0.2416
Average B factor: 29.656
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES/NaOH pH 7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.86
Solvent content (%): 57.06
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-03-09
CYCLIC GMP-AMP SYNTHASE in complex with compound 16 inhibitor: 7-hydroxy-N-methyl-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide (PDB entry 6NFG)
Macromolecule: CYCLIC GMP-AMP SYNTHASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.182
R free: 0.244
Average B factor: 50.92
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: PROTEIN WAS CONCENTRATED TO 6 MG/ML,
AND THEN MIXED AT A 2:1 RATIO WITH PEG 3350 (18-20% V/V), 0.2 M
 AMMONIUM CITRATE (PH 7) IN A SITTING DROP WELL AT 277 K.
 CRYOPROTECTANT WAS MADE USING MOTHER LIQUOR AT A FINAL
 CONCENTRATION OF 23% PEG 3350, VAPOR DIFFUSION, SITTING DROP,
 TEMPERATURE 277K
Matthews coefficient: 2.44
Solvent content (%): 49.59
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-01-23
Crystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder in P21 space group (PDB entry 7TYD)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 132 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSPHRPILQAGLPANTTAVVGSDVELLCKVYSDAQPHIQWLKHIVINGSSFGADGFPYVQVLKTADINSSEVEVLYLRNVSAEDAGEYTCLAGNSIGLSYQSAWLTVLPEED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.86
R work: 0.2684
R free: 0.3063
Average B factor: 58.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 5.5)
25% polyethylene glycol 3,350
3% 1,5-diaminopentane dihydrochloride
Matthews coefficient: 2.26
Solvent content (%): 45.5
Release date: 2022-11-09
Histone deacetylases complex with peptide macrocycles (PDB entry 6WHO)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 385 residues
Sequence: AAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1842
R free: 0.2207
Average B factor: 41.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 40 % PEG600 and 100mM CHES pH 9.5
Matthews coefficient: 2.39
Solvent content (%): 48.62
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-04-21
Crystal structure of a superbinder Fes SH2 domain (sFesS) in complex with a high affinity phosphopeptide (PDB entry 7T1L)
Macromolecule: Tyrosine-protein kinase Fes/Fps
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 100 residues
Sequence: GKPLHEQLWYHGAIPRAEVAELLVHSGDFLVRESETVKGAYALSVLWDGLPRHFLIQSLDNLYRLEGEGFPSIPLLIDHLLSTQQPLTKKSGVVLHRAVP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.164
R free: 0.1973
Average B factor: 22.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M Sodium Citrate Tribasic Dihydrate and 100 mM Bis-Tris Propane (pH=8.5)
Matthews coefficient: 1.87
Solvent content (%): 34.35
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-08-24
The crystal structure of PAK1 with the inhibitor GW8510 (PDB entry 7VTO)
Macromolecule: Serine/threonine-protein kinase PAK 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: GSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNHGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.235
R free: 0.2519
Average B factor: 73.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris pH 8.5, 0.2 MgCl2, 24% PEG 3350, 5 mM TCEP
Matthews coefficient: 2.46
Solvent content (%): 49.98
Ligand: 4-[(7-OXO-7H-THIAZOLO[5,4-E]INDOL-8-YLMETHYL)-AMINO]-N-PYRIDIN-2-YL-BENZENESULFONAMIDE (107)
Ligand formula: C21 H15 N5 O3 S2
Ligand molecular weight: 449.506
Ligand SMILES: c1ccnc(c1)NS(=O)(=O)c2ccc(cc2)NCC3=C4c5c(ncs5)C=CC4=NC3=O
Ligand InChI: InChI=1S/C21H15N5O3S2/c27-21-15(19-16(25-21)8-9-17-20(19)30-12-24-17)11-23-13-4-6-14(7-5-13)31(28,29)26-18-3-1-2-10-22-18/h1-10,12,23H,11H2,(H,22,26)
Release date: 2022-11-02
The ubiquitin-associated domain of human thirty-eight negative kinase 1, flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at low protein concentration (PDB entry 7TDY)
Macromolecule: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 155 residues
Sequence: GSIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLSPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDELYELLQHILGGELQRKIMEVELSVHGVTHQEAQTALGATGGDVVSAIRNLKVDQLFHLSSRSRADAWRILEHYQWDLSAASRYVLARP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.2052
R free: 0.2174
Average B factor: 40.22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 1.2 uL of 2 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 7.00, 250 mM Mg-Formate.
Matthews coefficient: 2.24
Solvent content (%): 45.12
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-01-11
CRYSTAL STRUCTURE OF c-MET IN COMPLEX WITH NOVEL INHIBITOR (PDB entry 5YA5)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 319 residues
Sequence: MGSSHHHHHHGDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.2114
R free: 0.2349
Average B factor: 38.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris pH7.5, 15% glycerol, 12% MPD, 5% isopropanol, 15% PEG5Kmme
Matthews coefficient: 2.21
Solvent content (%): 44.29
Ligand: 2-[3-(4-methoxybenzyl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazol-6-yl]-1H-indole (6TD)
Ligand formula: C19 H15 N5 O S
Ligand molecular weight: 361.42
Ligand SMILES: COc1ccc(cc1)Cc2nnc3n2nc(s3)c4cc5ccccc5[nH]4
Ligand InChI: InChI=1S/C19H15N5OS/c1-25-14-8-6-12(7-9-14)10-17-21-22-19-24(17)23-18(26-19)16-11-13-4-2-3-5-15(13)20-16/h2-9,11,20H,10H2,1H3
Release date: 2018-07-04
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster2 (PDB entry 7GTX)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.2002
R free: 0.2217
Average B factor: 38.2885
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.84
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-31
Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 5-IP7 (PDB entry 6PCL)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 148 residues
Sequence: MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1429
R free: 0.1609
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 290.15
Crystal growth procedure: 12 - 18% PEG 8000, 150 - 300 mM LiSO4, 0.1 M sodium acetate, pH 4.6
Matthews coefficient: 2.47
Solvent content (%): 50.25
Ligand: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate (I7P)
Ligand formula: C6 H19 O27 P7
Ligand molecular weight: 740.015
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2+,3-,4-,5+,6+
Release date: 2020-04-29
An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C (PDB entry 5G03)
Macromolecule: CARBONIC ANHYDRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVDKALQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAEGVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1275
R free: 0.16005
Average B factor: 15.29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 150 NL PROTEIN AT 5.5 MG/ML PLUS 120 NL RESERVOIR AND 30 NL SEEDS IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE PLUS 100 MM TRIS PH 8.5
Matthews coefficient: 2.09
Solvent content (%): 41.2
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2016-05-25
Hsp90 alpha inhibitor (PDB entry 7UR3)
Macromolecule: Heat shock protein HSP 90-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 293 residues
Sequence: MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAEEKEDKEEEKEKEEKESEDKPEIEDVGSDEEEEKKDGDKKKKKKIKEKYIDQEELNKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1742
R free: 0.1885
Average B factor: 31.5138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEGMME 2000, 0.2 M magnesium chloride, and 0.1 M sodium cacodylate pH 6.5
Matthews coefficient: 2.11
Solvent content (%): 41.6
Ligand: (5-fluoro-1,3-dihydro-2H-isoindol-2-yl){4-hydroxy-3-[(2S)-2-hydroxy-5-phenylpentan-2-yl]phenyl}methanone (OJ3)
Ligand formula: C26 H26 F N O3
Ligand molecular weight: 419.488
Ligand SMILES: CC(CCCc1ccccc1)(c2cc(ccc2O)C(=O)N3Cc4ccc(cc4C3)F)O
Ligand InChI: InChI=1S/C26H26FNO3/c1-26(31,13-5-8-18-6-3-2-4-7-18)23-15-19(10-12-24(23)29)25(30)28-16-20-9-11-22(27)14-21(20)17-28/h2-4,6-7,9-12,14-15,29,31H,5,8,13,16-17H2,1H3/t26-/m0/s1
Release date: 2022-12-28
SOD1 and Nanobody3 complex (PDB entry 8K3L)
Macromolecule: Superoxide dismutase [Cu-Zn]
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.15.1.1
Sequence length: 153 residues
Sequence: ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.195
R free: 0.2347
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v
Polyethylene, glycol monomethyl ether 2,000
Matthews coefficient: 2.63
Solvent content (%): 53.23
Ligand: COPPER (II) ION (CU)
Ligand formula: Cu
Ligand molecular weight: 63.546
Ligand SMILES: [Cu+2]
Ligand InChI: InChI=1S/Cu/q+2
Release date: 2024-07-17
CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 6-((R)-2-o-Tolyloxymethyl-pyrrolidin-1-yl)-9H-purine (PDB entry 5LYW)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 378 residues
Sequence: MGPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDYHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.171
R free: 0.193
Average B factor: 40.44
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 24% methanol, 100 mM citrate
Matthews coefficient: 2.66
Solvent content (%): 53.73
Ligand: 6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine (7BH)
Ligand formula: C17 H19 N5 O
Ligand molecular weight: 309.366
Ligand SMILES: Cc1ccccc1OCC2CCCN2c3c4c(nc[nH]4)ncn3
Ligand InChI: InChI=1S/C17H19N5O/c1-12-5-2-3-7-14(12)23-9-13-6-4-8-22(13)17-15-16(19-10-18-15)20-11-21-17/h2-3,5,7,10-11,13H,4,6,8-9H2,1H3,(H,18,19,20,21)/t13-/m1/s1
Release date: 2017-08-16
Ternary complex of DNA polymerase Mu with 1-nt gapped DNA (T:dGMPNPP) and Mn (PDB entry 7COA)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 482 residues
Sequence: MLPKRRRARVGSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.698
R work: 0.175
R free: 0.1991
Average B factor: 26.8868
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: TRIS-HCL, PEG 3350
Matthews coefficient: 1.93
Solvent content (%): 36.37
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2021-06-30
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with P11 (PDB entry 5QIO)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1725
R free: 0.1974
Average B factor: 18.261
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.28
Solvent content (%): 46.09
Ligand: Unknown ligand (UNL)
Release date: 2019-12-18
New method for synthesis of benzoxazole amide inhibitors of carbonic anhydrase (PDB entry 5TFX)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.18661
R free: 0.24619
Average B factor: 13.662
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: 2.7 M ammonium sulfate, 100 mM Tris pH 8.3 with protein at 7 mg/mL
Matthews coefficient: 2.11
Solvent content (%): 41.8
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-08-09
Crystal structure of complex of urokinase and a upain-1 variant(W3F) in pH7.4 condition (PDB entry 6XVD)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1863
R free: 0.2025
Average B factor: 14.578
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M sodium citrate at pH 4.5, 1.95 M (NH4)2SO4, 0.05% NaN3, and 5% PEG400
Matthews coefficient: 2.04
Solvent content (%): 39.76
Release date: 2020-02-19
CA II in complex with the coumarin benzene sulfonamide SG1-51 (PDB entry 8SAF)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.23
R work: 0.2159
R free: 0.237
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM tris base
Matthews coefficient: 2.08
Solvent content (%): 40.83
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-04-03