satarupa22/MacromolecularLigandDB huggingface dataset:
DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 960 min (PDB entry 7M4G)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.2115
R free: 0.2395
Average B factor: 55.727
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.83
Solvent content (%): 56.6
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-07-06
Human DNA polymerase eta R61A-DNA ternary complex: reaction with 1 mM Mg2+ for 140s (PDB entry 5KFV)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTASMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.196
R free: 0.229
Average B factor: 23.64
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.12
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2016-06-22
Crystal structure of the DNA polymerase lambda binary complex (PDB entry 5IIO)
Macromolecule: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: CGGCGGTACTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.1913
R free: 0.2351
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
Matthews coefficient: 2.89
Solvent content (%): 57.47
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-08-17
The FK1 domain of FKBP51 in complex with SAFit-analog 24e (PDB entry 9EUB)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2393
R free: 0.2772
Average B factor: 40.351
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG3350, 0.2M sodium thiocyanate, 0.1M HEPES-NaOH pH 7.5 10% ethylene glycol
Matthews coefficient: 2.41
Solvent content (%): 48.94
Ligand: [1-(2-hydroxyethyl)pyrazol-4-yl]methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate (A1H7E)
Ligand formula: C29 H41 N3 O7
Ligand molecular weight: 543.652
Ligand SMILES: COc1cc(cc(c1OC)OC)C(C2CCCCC2)C(=O)N3CCCCC3C(=O)OCc4cnn(c4)CCO
Ligand InChI: InChI=1S/C29H41N3O7/c1-36-24-15-22(16-25(37-2)27(24)38-3)26(21-9-5-4-6-10-21)28(34)32-12-8-7-11-23(32)29(35)39-19-20-17-30-31(18-20)13-14-33/h15-18,21,23,26,33H,4-14,19H2,1-3H3/t23-,26-/m0/s1
Release date: 2024-06-12
Crystal structure of human DNA cross-link repair 1A in complex with quinoxalinedione inhibitor H2 (PDB entry 8CF0)
Macromolecule: DNA cross-link repair 1A protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.2.6
Sequence length: 345 residues
Sequence: SMKKTCPFYKKIPGTGFTVDAFQYGVVEGCTAYFLTHFHSDHYAGLSKHFTFPVYCSEITGNLLKNKLHVQEQYIHPLPLDTECIVNGVKVVLLDANHCPGAVMILFYLPNGTVILHTGDFRADPSMERSLLADQKVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVTLNPHALVVCGTYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCSSLVHLLPMMQINFKGLQSHLKKCGGKYNQILAFRPTGWTHSNKFTRIADVIPQTKGNISIYGIPYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRSTMEKYFREWKLEAGY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.2196
R free: 0.2567
Average B factor: 30.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 1000, 0.1M MIB buffer
Matthews coefficient: 2.11
Solvent content (%): 41.61
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2024-02-21
PRMT5/MEP50 crystal structure with MTA and MRTX-1719 bound (PDB entry 7S1S)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.2086
R free: 0.2332
Average B factor: 63.82
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 281
Crystal growth procedure: 100 mM Sodium Citrate pH 5.4, 11% PEG 4000, 50 mM Sodium Acetate
Matthews coefficient: 2.85
Solvent content (%): 56.87
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2022-01-26
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000465a (PDB entry 5QDW)
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): 2.212
R work: 0.186
R free: 0.221
Average B factor: 45.7267
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.19
Ligand: 2-methoxy-N-[(1R)-1-phenylethyl]acetamide (JGJ)
Ligand formula: C11 H15 N O2
Ligand molecular weight: 193.242
Ligand SMILES: CC(c1ccccc1)NC(=O)COC
Ligand InChI: InChI=1S/C11H15NO2/c1-9(12-11(13)8-14-2)10-6-4-3-5-7-10/h3-7,9H,8H2,1-2H3,(H,12,13)/t9-/m1/s1
Release date: 2018-10-10
Human DNA polymerase lambda L431A mutant- MgdCTP binary and complex with 6 paired DNA (PDB entry 5CR0)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 334 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVAITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2427
R free: 0.2815
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Matthews coefficient: 2.63
Solvent content (%): 53.22
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2016-02-24
Crystal structure of Bruton agammabulinemia tyrosine kinase complexed with BMS-986142 aka (2s)-6-fluoro-5-[3-(8-fluoro-1-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-3-yl)-2-methylphenyl]-2-(2-hydroxypropan-2-yl)-2,3,4,9-tetrahydro-1h-carbazole-8-carboxamide (PDB entry 5T18)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 267 residues
Sequence: GHMEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.203
R free: 0.223
Average B factor: 24.9
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG8K + 3% MEPEG5K + 0.2M TRIS-HCL, PH 7.0
Matthews coefficient: 2.32
Solvent content (%): 46.91
Ligand: 6-Fluoro-5-(R)-(3-(S)-(8-fluoro-1-methyl-2,4-dioxo-1,2-dihydroquinazolin-3(4H)-yl)-2-methylphenyl)-2-(S)-(2-hydroxypropan-2-yl)-2,3,4,9-tetrahydro-1H-carbazole-8-carboxamide (73T)
Ligand formula: C32 H30 F2 N4 O4
Ligand molecular weight: 572.602
Ligand SMILES: Cc1c(cccc1N2C(=O)c3cccc(c3N(C2=O)C)F)c4c(cc(c5c4c6c([nH]5)CC(CC6)C(C)(C)O)C(=O)N)F
Ligand InChI: InChI=1S/C32H30F2N4O4/c1-15-17(7-6-10-24(15)38-30(40)19-8-5-9-21(33)28(19)37(4)31(38)41)25-22(34)14-20(29(35)39)27-26(25)18-12-11-16(32(2,3)42)13-23(18)36-27/h5-10,14,16,36,42H,11-13H2,1-4H3,(H2,35,39)/t16-/m0/s1
Release date: 2017-03-08
Crystal structure of SMYD3 with SAM and EPZ028862 (PDB entry 5V37)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 428 residues
Sequence: MEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.2276
R free: 0.2789
Average B factor: 18.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350
Matthews coefficient: 2.2
Solvent content (%): 44.07
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: 2018-03-07
Cathepsin-K in complex with amino-oxaazabicyclo[3.3.0]octanyl containing inhibitor (PDB entry 6QM0)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 216 residues
Sequence: RAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1307
R free: 0.174
Average B factor: 24.819
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.1
Crystallization temperature (K): 291
Crystal growth procedure: 25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
Matthews coefficient: 2.06
Solvent content (%): 40.35
Ligand: (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID (MHA)
Ligand formula: C6 H10 N2 O5
Ligand molecular weight: 190.154
Ligand SMILES: C(C(=O)N)N(CC(=O)O)CC(=O)O
Ligand InChI: InChI=1S/C6H10N2O5/c7-4(9)1-8(2-5(10)11)3-6(12)13/h1-3H2,(H2,7,9)(H,10,11)(H,12,13)
Release date: 2020-02-19
Co-crystal structure of BTK kinase domain with inhibitor (PDB entry 7YC9)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 269 residues
Sequence: GSGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1656
R free: 0.1874
Average B factor: 13.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Sodium cacodylate trihydrate pH 7.0, 0.2M Ammonium sulfate, 26% PEG8000
Matthews coefficient: 2.35
Solvent content (%): 47.71
Ligand: (7~{S})-2-(4-bromanyl-3,5-dimethoxy-phenyl)-7-(1-propanoylpiperidin-4-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide (IS4)
Ligand formula: C23 H30 Br N5 O4
Ligand molecular weight: 520.419
Ligand SMILES: CCC(=O)N1CCC(CC1)C2CCNc3n2nc(c3C(=O)N)c4cc(c(c(c4)OC)Br)OC
Ligand InChI: InChI=1S/C23H30BrN5O4/c1-4-18(30)28-9-6-13(7-10-28)15-5-8-26-23-19(22(25)31)21(27-29(15)23)14-11-16(32-2)20(24)17(12-14)33-3/h11-13,15,26H,4-10H2,1-3H3,(H2,25,31)/t15-/m0/s1
Release date: 2023-05-17
FKBP12-FRB in Complex with Compound 11 (PDB entry 8ER6)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 107 residues
Sequence: GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.81
R work: 0.2007
R free: 0.2241
Average B factor: 74.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3.0-3.3 M sodium formate and 0.1 M HEPES pH 7.0-7.5
Matthews coefficient: 4.11
Solvent content (%): 70.09
Ligand: (3S,5R,6R,7E,9R,10R,12R,14S,15E,17E,19E,21S,23S,26R,27R,30R,34aS)-5,9,27-trihydroxy-3-{(2R)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-5,6,9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-octadecahydro-3H-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontine-1,11,28,29(4H,31H)-tetrone (XYU)
Ligand formula: C51 H81 N O13
Ligand molecular weight: 916.188
Ligand SMILES: CC1CCC2CC(C(=CC=CC=CC(CC(C(=O)C(C(C(=CC(C(CC(OC(=O)C3CCCCN3C(=O)C(=O)C1(O2)O)C(C)CC4CCC(C(C4)OC)O)O)C)C)O)OC)C)C)C)OC
Ligand InChI: InChI=1S/C51H81NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-44,46-47,53-54,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33-,34-,36-,37+,38+,39+,40-,41-,42+,43+,44-,46-,47+,51-/m1/s1
Release date: 2022-12-28
PCSK9 in complex with compound 4 (PDB entry 6U2N)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 707 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.19
R free: 0.234
Average B factor: 47.23
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 303
Crystal growth procedure: (10-22)% PEG 10000, 0.1M Tris, pH 8.5, 10% Ethylene Glycol, 1% BAM
Matthews coefficient: 2.69
Solvent content (%): 54.25
Ligand: 4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid (PV7)
Ligand formula: C23 H23 N3 O5 S
Ligand molecular weight: 453.511
Ligand SMILES: CC1(c2cc(c(cc2CCN1)OC)Oc3ccc(cc3)C(=O)O)CC(=O)Nc4nccs4
Ligand InChI: InChI=1S/C23H23N3O5S/c1-23(13-20(27)26-22-24-9-10-32-22)17-12-19(18(30-2)11-15(17)7-8-25-23)31-16-5-3-14(4-6-16)21(28)29/h3-6,9-12,25H,7-8,13H2,1-2H3,(H,28,29)(H,24,26,27)/t23-/m1/s1
Release date: 2019-11-06
Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications (PDB entry 6J4Q)
Macromolecule: Tubulinyl-Tyr carboxypeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.17
Sequence length: 251 residues
Sequence: GVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILGIYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTLSDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKILK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1835
R free: 0.247
Crystallization method: EVAPORATION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.
Matthews coefficient: 2.79
Solvent content (%): 55.91
Ligand: N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide (TQ8)
Ligand formula: C17 H18 Cl N O3 S
Ligand molecular weight: 351.848
Ligand SMILES: Cc1ccc(cc1)S(=O)(=O)NC(Cc2ccccc2)C(=O)CCl
Ligand InChI: InChI=1S/C17H18ClNO3S/c1-13-7-9-15(10-8-13)23(21,22)19-16(17(20)12-18)11-14-5-3-2-4-6-14/h2-10,16,19H,11-12H2,1H3/t16-/m0/s1
Release date: 2019-05-01
Crystal structure of human tankyrase 2 in complex with TA-49 (PDB entry 4UI7)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 49 residues
Sequence: AMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16725
R free: 0.1998
Average B factor: 27.4
Crystallization pH: 8.5
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5
Matthews coefficient: 2.4
Solvent content (%): 50
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: 2016-04-13
Closo-carborane ethyl-sulfonamide in complex with CA II (PDB entry 6YZV)
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): 1.65
R work: 0.1768
R free: 0.2044
Average B factor: 19.895
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris
1.6 M Natrium Citrate
Matthews coefficient: 2.07
Solvent content (%): 40.61
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: 2020-10-28
Crystal structure of human sarcomeric mitochondrial creatine kinase (PDB entry 4Z9M)
Macromolecule: Creatine kinase S-type, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.3.2
Sequence length: 392 residues
Sequence: GSTTGYLLNRQKVCAEVREQPRLFPPSADYPDLRKHNNCMAECLTPAIYAKLRNKVTPNGYTLDQCIQTGVDNPGHPFIKTVGMVAGDEESYEVFADLFDPVIKLRHNGYDPRVMKHTTDLDASKITQGQFDEHYVLSSRVRTGRSIRGLSLPPACTRAERREVENVAITALEGLKGDLAGRYYKLSEMTEQDQQRLIDDHFLFDKPVSPLLTCAGMARDWPDARGIWHNYDKTFLIWINEEDHTRVISMEKGGNMKRVFERFCRGLKEVERLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHVRIPKLSKDPRFSKILENLRLQKRGTGGVDTAAVADVYDISNIDRIGRSEVELVQIVIDGVNYLVDCEKKLERGQDIKVPPPLPQF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2023
R free: 0.2362
Average B factor: 38.291
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 17% PEG-3350, 10mM DTT, 0.2M diammonium citrate, 0.1M Bis-TRIS, protein buffer also contained magnesium chloride, creatine, ADP
Matthews coefficient: 2.78
Solvent content (%): 55.7
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2015-04-22