Structure of PDB 6dyz Chain A Binding Site BS02

Receptor Information
>6dyz Chain A (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCVLL
ARHGRQHTIMPSKVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIV
IIDQFIDRTTMRPQSFYDGSHSCARGVCHIPMAEPFCPKTREVLIETAKK
LGLRCHSKGTMVTIEGPRFSSRAESFMFRTWGADVINMTTVPEVVLAKEA
GICYASIAMATDYDCWKEHEEAVSVDRVLKTLKENANKAKSLLLTTIPQI
GSTEWSETLHNLKNMAQFSVLLP
Ligand information
Ligand IDOS2
InChIInChI=1S/C15H19N5OS/c1-2-3-22-8-11-6-20(7-12(11)21)5-10-4-17-14-13(10)18-9-19-15(14)16/h1,4,9,11-12,17,21H,3,5-8H2,(H2,16,18,19)/t11-,12+/m1/s1
InChIKeyMQJBNGGMAUMWEV-NEPJUHHUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C#CCSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
CACTVS 3.385Nc1ncnc2c(CN3C[CH](O)[CH](CSCC#C)C3)c[nH]c12
OpenEye OEToolkits 2.0.6C#CCSCC1CN(CC1O)Cc2c[nH]c3c2ncnc3N
ACDLabs 12.01OC3CN(Cc2c1ncnc(c1nc2)N)CC3CSCC#C
CACTVS 3.385Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCC#C)C3)c[nH]c12
FormulaC15 H19 N5 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(prop-2-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol
ChEMBLCHEMBL4445386
DrugBank
ZINC
PDB chain6dyz Chain A Residue 307 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dyz Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Resolution1.62 Å
Binding residue
(original residue number in PDB)		T18 H65 A94 C95 G96 F177 I194 N195 M196 D220 D222 V236
Binding residue
(residue number reindexed from 1)		T10 H57 A86 C87 G88 F169 I186 N187 M188 D212 D214 V228
Annotation score1
Binding affinityMOAD: Kd=0.63nM
PDBbind-CN: -logKd/Ki=9.20,Kd=0.63nM
BindingDB: Kd=0.630000nM
Enzymatic activity
Catalytic site (original residue number in PDB) T18 P41 H65 I67 M68 A94 M196 T197 D220 D222 V233
Catalytic site (residue number reindexed from 1) T10 P33 H57 I59 M60 A86 M188 T189 D212 D214 V225
Enzyme Commision number 2.4.2.28: S-methyl-5'-thioadenosine phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
GO:0017061 S-methyl-5-thioadenosine phosphorylase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006166 purine ribonucleoside salvage
GO:0006738 nicotinamide riboside catabolic process
GO:0009116 nucleoside metabolic process
GO:0019509 L-methionine salvage from methylthioadenosine
GO:0032259 methylation
GO:0033574 response to testosterone
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6dyz, PDBe:6dyz, PDBj:6dyz
PDBsum6dyz
PubMed30860833
UniProtQ13126|MTAP_HUMAN S-methyl-5'-thioadenosine phosphorylase (Gene Name=MTAP)

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