Structure of PDB 3rw9 Chain B Binding Site BS01

Receptor Information
>3rw9 Chain B (length=282) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLV
LDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKH
PSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQ
DAFDVIITDSSGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLI
KEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLT
QQQVAQMQLKYYNSDVHRAAFVLPEFARKALN
Ligand information
Ligand IDDSH
InChIInChI=1S/C13H20N6O3S/c14-2-1-3-23-4-7-9(20)10(21)13(22-7)19-6-18-8-11(15)16-5-17-12(8)19/h5-7,9-10,13,20-21H,1-4,14H2,(H2,15,16,17)/t7-,9-,10-,13-/m1/s1
InChIKeyFUSRAALGPJJIRO-QYVSTXNMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCCN)O)O)N
CACTVS 3.370NCCCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
CACTVS 3.370NCCCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSCCCN)N
OpenEye OEToolkits 1.7.2c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCCCN)O)O)N
FormulaC13 H20 N6 O3 S
Name5'-S-(3-aminopropyl)-5'-thioadenosine
ChEMBLCHEMBL538693
DrugBank
ZINCZINC000005163039
PDB chain3rw9 Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3rw9 Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Q49 Q70 G101 G103 E124 I125 D155 G156 D173 S174 S175 P180 A181 L184
Binding residue
(residue number reindexed from 1)		Q35 Q56 G87 G89 E110 I111 D141 G142 D159 S160 S161 P163 A164 L167
Annotation score3
Binding affinityMOAD: Kd=1.1uM
Enzymatic activity
Enzyme Commision number 2.5.1.16: spermidine synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004766 spermidine synthase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006595 polyamine metabolic process
GO:0008295 spermidine biosynthetic process
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3rw9, PDBe:3rw9, PDBj:3rw9
PDBsum3rw9
PubMed21898642
UniProtP19623|SPEE_HUMAN Spermidine synthase (Gene Name=SRM)

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