satarupa22/MacromolecularLigandDB huggingface dataset:
The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a (PDB entry 5ZXF)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 87 residues
Sequence: QETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.2178
R free: 0.2431
Average B factor: 20.887
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M NaOAc, 1.2M AmSO4, Seeding.
Matthews coefficient: 2.41
Solvent content (%): 49
Ligand: 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one (NUT)
Ligand formula: C30 H30 Cl2 N4 O4
Ligand molecular weight: 581.49
Ligand SMILES: CC(C)Oc1cc(ccc1C2=NC(C(N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC
Ligand InChI: InChI=1S/C30H30Cl2N4O4/c1-18(2)40-25-16-23(39-3)12-13-24(25)29-34-27(19-4-8-21(31)9-5-19)28(20-6-10-22(32)11-7-20)36(29)30(38)35-15-14-33-26(37)17-35/h4-13,16,18,27-28H,14-15,17H2,1-3H3,(H,33,37)/t27-,28+/m0/s1
Release date: 2018-08-22
CDK2 in complex with FragLite13 (PDB entry 6Q4B)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.12
R work: 0.17272
R free: 0.20326
Average B factor: 22.825
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Matthews coefficient: 2
Solvent content (%): 38.47
Ligand: 5-bromanylpyrimidine (HHN)
Ligand formula: C4 H3 Br N2
Ligand molecular weight: 158.984
Ligand SMILES: c1c(cncn1)Br
Ligand InChI: InChI=1S/C4H3BrN2/c5-4-1-6-3-7-2-4/h1-3H
Release date: 2019-03-20
Crystal structure of mutant cMET D1228N kinase domain in complex with inhibitor compound 13 (PDB entry 9C1R)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 307 residues
Sequence: MQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARNMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1686
R free: 0.1947
Average B factor: 15.86
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG 3350
0.1M Bis-Tris pH6.5
Matthews coefficient: 1.95
Solvent content (%): 36.84
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2024-08-21
Crystal structure of DAPK1 in complex with ANS. (PDB entry 5AUT)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1703
R free: 0.2024
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.91
Solvent content (%): 35.56
Ligand: 8-ANILINO-1-NAPHTHALENE SULFONATE (2AN)
Ligand formula: C16 H13 N O3 S
Ligand molecular weight: 299.344
Ligand SMILES: c1ccc(cc1)Nc2cccc3c2c(ccc3)S(=O)(=O)O
Ligand InChI: InChI=1S/C16H13NO3S/c18-21(19,20)15-11-5-7-12-6-4-10-14(16(12)15)17-13-8-2-1-3-9-13/h1-11,17H,(H,18,19,20)
Release date: 2015-10-07
c-KIT kinase domain in complex with avapritinib (PDB entry 8PQ9)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1905
R free: 0.2044
Average B factor: 41.49
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 285.15
Crystal growth procedure: 6.6 mg/mL, 10% PEG8000, 20% Ethylen glycole, 30 mM NaI, 30 mM NaF, 30 mM NaBr, 100 mM Bicine, pH 8.5
Matthews coefficient: 1.93
Solvent content (%): 36.4
Ligand: Avapritinib (9JI)
Ligand formula: C26 H27 F N10
Ligand molecular weight: 498.558
Ligand SMILES: CC(c1ccc(cc1)F)(c2cnc(nc2)N3CCN(CC3)c4c5cc(cn5ncn4)c6cnn(c6)C)N
Ligand InChI: InChI=1S/C26H27FN10/c1-26(28,20-3-5-22(27)6-4-20)21-13-29-25(30-14-21)36-9-7-35(8-10-36)24-23-11-18(16-37(23)33-17-31-24)19-12-32-34(2)15-19/h3-6,11-17H,7-10,28H2,1-2H3/t26-/m0/s1
Release date: 2023-12-27
Crystal structure of FGFR4 kinase domain with 10t (PDB entry 7YC3)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GPLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.987
R work: 0.1616
R free: 0.196
Average B factor: 28.5586
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.88
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: 2022-11-16
DNA Polymerase Mu Reactant Complex, 10 mM Mg2+ (45 min) (PDB entry 5TYD)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.899
R work: 0.171
R free: 0.2116
Average B factor: 22.759
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.68
Solvent content (%): 54.03
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: 2017-08-30
Crystal structure of mouse CARM1 in complex with ligand P1C3u (PDB entry 5LGR)
Macromolecule: Histone-arginine methyltransferase CARM1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.1.1.319
Sequence length: 361 residues
Sequence: GHMGHTLERSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPPG
Oligomeric state: Hetero 8-mer
Stoichiometry: A4, B3, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.192
R free: 0.2337
Average B factor: 42.9158
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Tris-HCl pH 8.5 100 mM
PEG 3350 14 %
Ammonium Sulfate 200 mM
Matthews coefficient: 2.32
Solvent content (%): 47.08
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: 2017-03-22
Crystal Structure of human phosphodiesterase 10 in complex with 3-methyl-6-[2-(1-methyl-4-phenylimidazol-2-yl)ethyl]-2-(trifluoromethyl)imidazo[1,2-b]pyridazine (PDB entry 5SEM)
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): 2.1
R work: 0.1778
R free: 0.2276
Average B factor: 43.861
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: 2.64
Solvent content (%): 53.36
Ligand: (4S)-3-methyl-6-[2-(1-methyl-4-phenyl-1H-imidazol-2-yl)ethyl]-2-(trifluoromethyl)imidazo[1,2-b]pyridazine (IG6)
Ligand formula: C20 H18 F3 N5
Ligand molecular weight: 385.386
Ligand SMILES: Cc1c(nc2n1nc(cc2)CCc3nc(cn3C)c4ccccc4)C(F)(F)F
Ligand InChI: InChI=1S/C20H18F3N5/c1-13-19(20(21,22)23)25-18-11-9-15(26-28(13)18)8-10-17-24-16(12-27(17)2)14-6-4-3-5-7-14/h3-7,9,11-12H,8,10H2,1-2H3
Release date: 2022-10-12
Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-beta-pNP (PDB entry 5GGK)
Macromolecule: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1
Sequence length: 164 residues
Sequence: GPLGSGSGPRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1462
R free: 0.1755
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Tris-HCl, PEG-10000
Matthews coefficient: 2.39
Solvent content (%): 48.44
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2016-08-10
Crystal structure of human inorganic pyrophosphatase with metal ions (PDB entry 7BTN)
Macromolecule: Inorganic pyrophosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.1
Sequence length: 309 residues
Sequence: HHHHHHGPNTEFALSLLREFMSGFSTEERAAPFSLEYRVFLKNEKGQYISPFHDIPIYADKDVFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIGVKVLGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEFKDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTLSESPFKCDPDAARAIVDALPPPCESACTVPTDVDKWFHHQKN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.382
R work: 0.1787
R free: 0.2104
Average B factor: 39.8589
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 20% PEG4000, 50mM magnesium acetate, pH 5.5
Matthews coefficient: 2.79
Solvent content (%): 55.91
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: 2020-10-21
Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor CS-R35 (PDB entry 6ES0)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 317 residues
Sequence: SMGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEITFLEAVIQLKKTKLQSV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2135
R free: 0.2576
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG Smear Low -- 0.1M MES pH 6.5 -- 0.05M magnesium acetate -- 0.05M magnesium chloride
Matthews coefficient: 2.48
Solvent content (%): 50.41
Ligand: 2-[2-fluoranyl-4-[[2-fluoranyl-4-[2-(methylcarbamoyl)pyridin-4-yl]oxy-phenyl]carbamoylamino]phenyl]sulfanylethanoic acid (BW8)
Ligand formula: C22 H18 F2 N4 O5 S
Ligand molecular weight: 488.464
Ligand SMILES: CNC(=O)c1cc(ccn1)Oc2ccc(c(c2)F)NC(=O)Nc3ccc(c(c3)F)SCC(=O)O
Ligand InChI: InChI=1S/C22H18F2N4O5S/c1-25-21(31)18-10-14(6-7-26-18)33-13-3-4-17(15(23)9-13)28-22(32)27-12-2-5-19(16(24)8-12)34-11-20(29)30/h2-10H,11H2,1H3,(H,25,31)(H,29,30)(H2,27,28,32)
Release date: 2018-02-21
Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine (PDB entry 5B5O)
Macromolecule: Collagenase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24
Sequence length: 172 residues
Sequence: EYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1638
R free: 0.1854
Average B factor: 15.5145
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100mM TrisHCl, 1500mM ammonium formate, 10.4% PEG8000
Matthews coefficient: 2.31
Solvent content (%): 46.79
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-01-18
CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN (PDB entry 5TXK)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 35,Ubiquitin carboxyl-terminal hydrolase 35
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 372 residues
Sequence: SELAGFYPRLMAKSDTGKIGLINLGNTSYVNSILQALFMASDFRHCVLRLTENNSQPLMTKLQWLFGFLEHSQRPAISPENFLSASWTPWFSPGTQQDCSEYLKYLLDRLHEEEKTGTRICQKLKQSSSPSPPEEPPAPSSTSVEKMFGGKIVTRICCLCCLNVSSREEAFTDLSLAFPPPGSEGSRSVLDLVNYFLSPEKLTAENRYYCESCASLQDAEKVVELSQGPCYLILTLLRFSFDLRTMRRRKILDDVSIPLLLRLPLAGGRGQAYDLCSVVVHSGVSSESGHYYCYAREGAARPAASLGTADRPEPENQWYLFNDTRVSFSSFESVSNVTSFFPKDTAYVLFYRQRPREGPEAELGSSRVRTEP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1602
R free: 0.1834
Average B factor: 25.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 296
Crystal growth procedure: 0.95 M ammonium sulphate
0.1 M HEPES
Matthews coefficient: 2.87
Solvent content (%): 57.16
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: 2018-05-09
Crystal structure of Aldo-keto reductase 1C3 complexed with compound 24 (PDB entry 7WQM)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 329 residues
Sequence: MHHHHHHDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.1719
R free: 0.2067
Average B factor: 22.5212
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: MES pH 6.0, Ammonium chloride, PEG 6000
Matthews coefficient: 2.23
Solvent content (%): 44.82
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-01-04
Structure of Ku80 von Willebrand domain complexed with APLF Ku Binding Motif (PDB entry 6TYZ)
Macromolecule: X-ray repair cross-complementing protein 5
Type: Protein, polypeptide(L)
Source organism: Xenopus laevis
EC number: 3.6.4
Sequence length: 231 residues
Sequence: MHHHHHHMARAAKSAVVLCMDVGLAMSHSNQGKESPFEQAKKVMMLFLQRQVFAESKDEIAVVLYGTDTTDNALAREDQYENISVHRHLMLPDFDLLEQIENVVEPGSVQADFLDALIVSMDLLQKETLGKKYTRLHIAVFSDLSSPFSVDQLEVIIANLKKAEITLQFFLPFSVDEGSGPGKGLSDQQKEGIEMVRKIMFSLDGEEGLSEVFTFRDSLERLSIFKKIERR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51076626452
R work: 0.177990078727
R free: 0.202557392373
Average B factor: 32.4861613002
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7.5, 20% (w/v) PEG4000
Matthews coefficient: 2.07
Solvent content (%): 40.53
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-11-27
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434926 (PDB entry 5RWI)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1772
R free: 0.1965
Average B factor: 17.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.12
Solvent content (%): 41.91
Ligand: 4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione (O3D)
Ligand formula: C9 H13 N O3 S
Ligand molecular weight: 215.269
Ligand SMILES: c1cc(oc1)CN2CCS(=O)(=O)CC2
Ligand InChI: InChI=1S/C9H13NO3S/c11-14(12)6-3-10(4-7-14)8-9-2-1-5-13-9/h1-2,5H,3-4,6-8H2
Release date: 2020-11-11
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13441a (PDB entry 5R59)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.1918
R free: 0.2697
Average B factor: 35.992
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 38.97
Ligand: methyl 3-(methylsulfonylamino)benzoate (6SU)
Ligand formula: C9 H11 N O4 S
Ligand molecular weight: 229.253
Ligand SMILES: COC(=O)c1cccc(c1)NS(=O)(=O)C
Ligand InChI: InChI=1S/C9H11NO4S/c1-14-9(11)7-4-3-5-8(6-7)10-15(2,12)13/h3-6,10H,1-2H3
Release date: 2020-07-01