Structure of PDB 6dz0 Chain A Binding Site BS02

Receptor Information
>6dz0 Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTAVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCV
LLARHGRQHTIMPSKVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGD
IVIIDQFIDRTTMRPQSFYDGSHSCARGVCHIPMAEPFCPKTREVLIETA
KKLGLRCHSKGTMVTIEGPRFSSRAESFMFRTWGADVINMTTVPEVVLAK
EAGICYASIAMATDYDCWKEHEEAVSVDRVLKTLKENANKAKSLLLTTIP
QIGSTEWSETLHNLKNMAQFSVLL
Ligand information
Ligand IDOS3
InChIInChI=1S/C17H23N5OS/c1-2-3-4-5-24-10-13-8-22(9-14(13)23)7-12-6-19-16-15(12)20-11-21-17(16)18/h1,6,11,13-14,19,23H,3-5,7-10H2,(H2,18,20,21)/t13-,14+/m1/s1
InChIKeyQRFSYYUFBJRRLL-KGLIPLIRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2c(CN3C[CH](O)[CH](CSCCCC#C)C3)c[nH]c12
CACTVS 3.385Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCC#C)C3)c[nH]c12
ACDLabs 12.01Nc1c2ncc(c2ncn1)CN3CC(O)C(C3)CSCCCC#C
OpenEye OEToolkits 2.0.6C#CCCCSCC1CN(CC1O)Cc2c[nH]c3c2ncnc3N
OpenEye OEToolkits 2.0.6C#CCCCSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
FormulaC17 H23 N5 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol
ChEMBLCHEMBL4465346
DrugBank
ZINC
PDB chain6dz0 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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PDB6dz0 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 T219 D220 D222 V233 V236
Binding residue
(residue number reindexed from 1)		T12 H59 A88 C89 G90 F171 I188 N189 M190 T213 D214 D216 V227 V230
Annotation score1
Binding affinityMOAD: Kd=0.94nM
PDBbind-CN: -logKd/Ki=9.03,Kd=0.94nM
BindingDB: Kd=0.940000nM
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) T12 P35 H59 I61 M62 A88 M190 T191 D214 D216 V227
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:6dz0, PDBe:6dz0, PDBj:6dz0
PDBsum6dz0
PubMed30860833
UniProtQ13126|MTAP_HUMAN S-methyl-5'-thioadenosine phosphorylase (Gene Name=MTAP)

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