Structure of PDB 4gdp Chain B Binding Site BS01

Receptor Information
>4gdp Chain B (length=502) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQG
RKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGR
VDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFL
TNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRAAFALNYDSVVQ
RIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQS
VLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCW
SNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQTSVTCWSQPL
FFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKC
LDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDD
PVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLK
LE
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain4gdp Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4gdp Mechanistic and Structural Analyses of the Roles of Active Site Residues in Yeast Polyamine Oxidase Fms1: Characterization of the N195A and D94N Enzymes.
Resolution1.9998 Å
Binding residue
(original residue number in PDB)		G15 G17 A19 E39 A40 R41 G46 R47 G62 A63 S64 W65 H67 V223 V253 P254 G270 W440 A449 Y450 G478 E479 G487 C488 A489 A492
Binding residue
(residue number reindexed from 1)		G9 G11 A13 E33 A34 R35 G40 R41 G56 A57 S58 W59 H61 V217 V247 P248 G264 W432 A441 Y442 G470 E471 G479 C480 A481 A484
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H67
Catalytic site (residue number reindexed from 1) H61
Enzyme Commision number 1.5.3.17: non-specific polyamine oxidase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0016491 oxidoreductase activity
GO:0046592 polyamine oxidase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0052897 N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity
GO:0052901 spermine oxidase activity
GO:0052903 N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity
Biological Process
GO:0006338 chromatin remodeling
GO:0015940 pantothenate biosynthetic process
GO:0046208 spermine catabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4gdp, PDBe:4gdp, PDBj:4gdp
PDBsum4gdp
PubMed23034052
UniProtP50264|FMS1_YEAST Polyamine oxidase FMS1 (Gene Name=FMS1)

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