Structure of PDB 3dz5 Chain A Binding Site BS01

Receptor Information
>3dz5 Chain A (length=245) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
cSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNF
MKPSHQGYPHRNFQEEIEFLNAIFPNGAAYCMGRMNSDCWYLYTLDSQPD
QTLEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATMFN
PCGYSMNGMKSDGTYWTIHITPEPEFSYVSFETNLSQTSYDDLIRKVVEV
FKPGKFVTTLFVNQSSQKIEGFKRLDCQSAMFNDYNFVFTSFAKK
Ligand information
Ligand IDM8M
InChIInChI=1S/C14H23N7O4/c1-7-19-9-12(15)17-6-18-13(9)21(7)14-11(23)10(22)8(25-14)5-20(2)3-4-24-16/h6,8,10-11,14,22-23H,3-5,16H2,1-2H3,(H2,15,17,18)/t8-,10-,11-,14-/m1/s1
InChIKeyMIGFZONTOHGZMB-IDTAVKCVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CCON)O)O)N
CACTVS 3.341CN(CCON)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23
OpenEye OEToolkits 1.5.0Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CCON)O)O)N
CACTVS 3.341CN(CCON)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2C)C3OC(C(O)C3O)CN(CCON)C)N
FormulaC14 H23 N7 O4
Name5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine
ChEMBLCHEMBL1187584
DrugBank
ZINCZINC000040379157
PDB chain3dz5 Chain A Residue 368 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dz5 New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine
Resolution2.43 Å
Binding residue
(original residue number in PDB)		X68 F223 C226 G227 Y228 S229 H243 I244 T245 E247
Binding residue
(residue number reindexed from 1)		X1 F149 C152 G153 Y154 S155 H169 I170 T171 E173
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.15,IC50=7nM
BindingDB: IC50=7nM
Enzymatic activity
Catalytic site (original residue number in PDB) S229 H243
Catalytic site (residue number reindexed from 1) S154 H168
Enzyme Commision number 4.1.1.50: adenosylmethionine decarboxylase.
Gene Ontology
Molecular Function
GO:0004014 adenosylmethionine decarboxylase activity
Biological Process
GO:0006597 spermine biosynthetic process
GO:0008295 spermidine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dz5, PDBe:3dz5, PDBj:3dz5
PDBsum3dz5
PubMed19209891
UniProtP17707|DCAM_HUMAN S-adenosylmethionine decarboxylase proenzyme (Gene Name=AMD1)

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