Structure of PDB 3c6m Chain D Binding Site BS02

Receptor Information
>3c6m Chain D (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRHSTLDFMLLRIYPHGLVLLDLQSRVKRLPPIVRGGAIDRYWPTADGRL
VEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAI
MGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKK
YMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVP
ISTSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLY
CPVEFSKEIVCVPSYLELWVFYTVWKKA
Ligand information
Ligand IDMTA
InChIInChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyWUUGFSXJNOTRMR-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
FormulaC11 H15 N5 O3 S
Name5'-DEOXY-5'-METHYLTHIOADENOSINE
ChEMBLCHEMBL277041
DrugBankDB02282
ZINCZINC000004228245
PDB chain3c6m Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3c6m Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		L164 N169 G198 G199 D201 E220 I221 V225 C256 D276 L277 T278 I282
Binding residue
(residue number reindexed from 1)		L83 N88 G117 G118 D120 E139 I140 V144 C175 D195 L196 T197 I201
Annotation score5
Binding affinityMOAD: Ki=0.3uM
Enzymatic activity
Enzyme Commision number 2.5.1.22: spermine synthase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016768 spermine synthase activity
Biological Process
GO:0006555 methionine metabolic process
GO:0006595 polyamine metabolic process
GO:0006596 polyamine biosynthetic process
GO:0006597 spermine biosynthetic process
GO:0008215 spermine metabolic process
Cellular Component
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:3c6m, PDBe:3c6m, PDBj:3c6m
PDBsum3c6m
PubMed18367445
UniProtP52788|SPSY_HUMAN Spermine synthase (Gene Name=SMS)

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