Structure of PDB 3dz6 Chain A Binding Site BS01

Receptor Information
>3dz6 Chain A (length=238) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
cSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNF
MKPSHQGYPHRNFQEEIEFLNAIFPNGAAYCMGRMNSDCWYLYTLDFDQT
LEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATMFNPC
GYSMNGMKSDGTYWTIHITPEPEFSYVSFETNLSQTSYDDLIRKVVEVFK
PGKFVTTLFVNIEGFKRLDCQSAMFNDYNFVFTSFAKK
Ligand information
Ligand IDM8E
InChIInChI=1S/C17H27N7O4/c1-3-11-22-12-15(18)20-9-21-16(12)24(11)17-14(26)13(25)10(28-17)8-23(2)6-4-5-7-27-19/h3,9-10,13-14,17,25-26H,1,4-8,19H2,2H3,(H2,18,20,21)/t10-,13-,14-,17-/m1/s1
InChIKeyXUKYGMIDWKBMIW-IWCJZZDYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN(CCCCON)CC1C(C(C(O1)n2c(nc3c2ncnc3N)C=C)O)O
OpenEye OEToolkits 1.5.0C[N@@](CCCCON)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2c(nc3c2ncnc3N)C=C)O)O
ACDLabs 10.04n2c1c(ncnc1n(c2\C=C)C3OC(C(O)C3O)CN(CCCCON)C)N
CACTVS 3.341CN(CCCCON)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C=C)nc3c(N)ncnc23
CACTVS 3.341CN(CCCCON)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C=C)nc3c(N)ncnc23
FormulaC17 H27 N7 O4
Name5'-{[4-(aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine
ChEMBL
DrugBankDB08163
ZINCZINC000053683388
PDB chain3dz6 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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PDB3dz6 New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine
Resolution1.83 Å
Binding residue
(original residue number in PDB)		X68 C82 F223 N224 C226 G227 Y228 I244 T245 E247
Binding residue
(residue number reindexed from 1)		X1 C15 F147 N148 C150 G151 Y152 I168 T169 E171
Annotation score1
Binding affinityMOAD: ic50=15nM
PDBbind-CN: -logKd/Ki=7.82,IC50=15nM
Enzymatic activity
Catalytic site (original residue number in PDB) S229 H243
Catalytic site (residue number reindexed from 1) S152 H166
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:3dz6, PDBe:3dz6, PDBj:3dz6
PDBsum3dz6
PubMed19209891
UniProtP17707|DCAM_HUMAN S-adenosylmethionine decarboxylase proenzyme (Gene Name=AMD1)

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