Structure of PDB 6dz2 Chain C Binding Site BS01

Receptor Information
>6dz2 Chain C (length=266) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCVLL
TIMPSKVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFID
RTTMRPQSFYDGSHSCARGVCHIPMAEPFCPKTREVLIETAKKLGLRCHS
KGTMVTIEGPRFSSRAESFMFRTWGADVINMTTVPEVVLAKEAGICYASI
AMATDYDCWKEHEEAVSVDRVLKTLKENANKAKSLLLTTIPQIGSTEWSE
TLHNLKNMAQFSVLLP
Ligand information
Ligand IDOS5
InChIInChI=1S/C24H30N8OS/c25-24-23-22(27-16-28-24)18(9-26-23)11-31-12-19(21(33)14-31)15-34-8-4-7-20-13-32(30-29-20)10-17-5-2-1-3-6-17/h1-3,5-6,9,13,16,19,21,26,33H,4,7-8,10-12,14-15H2,(H2,25,27,28)/t19-,21+/m1/s1
InChIKeyBROXRHKDLDDNBO-CTNGQTDRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)Cn2cc(nn2)CCCSCC3CN(CC3O)Cc4c[nH]c5c4ncnc5N
OpenEye OEToolkits 2.0.6c1ccc(cc1)Cn2cc(nn2)CCCSC[C@H]3CN(C[C@@H]3O)Cc4c[nH]c5c4ncnc5N
ACDLabs 12.01OC3CN(Cc1cnc2c1ncnc2N)CC3CSCCCc4nnn(c4)Cc5ccccc5
CACTVS 3.385Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCc4cn(Cc5ccccc5)nn4)C3)c[nH]c12
CACTVS 3.385Nc1ncnc2c(CN3C[CH](O)[CH](CSCCCc4cn(Cc5ccccc5)nn4)C3)c[nH]c12
FormulaC24 H30 N8 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol
ChEMBLCHEMBL4439603
DrugBank
ZINC
PDB chain6dz2 Chain C Residue 308 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6dz2 Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		T18 A94 C95 G96 F177 I194 N195 M196 D220 D222 V236 L240
Binding residue
(residue number reindexed from 1)		T10 A79 C80 G81 F162 I179 N180 M181 D205 D207 V221 L225
Annotation score1
Binding affinityMOAD: Kd=1.4nM
PDBbind-CN: -logKd/Ki=8.85,Kd=1.4nM
BindingDB: Kd=1.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) T18 P41 I67 M68 A94 M196 T197 D220 D222 V233
Catalytic site (residue number reindexed from 1) T10 P33 I52 M53 A79 M181 T182 D205 D207 V218
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:6dz2, PDBe:6dz2, PDBj:6dz2
PDBsum6dz2
PubMed30860833
UniProtQ13126|MTAP_HUMAN S-methyl-5'-thioadenosine phosphorylase (Gene Name=MTAP)

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