Structure of PDB 3cnt Chain A Binding Site BS01

Receptor Information
>3cnt Chain A (length=497) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGY
QGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEER
GRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQ
FLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSV
VQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVP
QSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEEC
CWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLERETSVTCWSQPLF
FVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCL
DSEDVIDGMRANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAM
SNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKLEHHH
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 chain3cnt Chain A Residue 517 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3cnt Crystal structure of fms1 in complex with R-Bz-MeSpermidine
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G15 G17 I18 A19 E39 A40 R41 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)		G11 G13 I14 A15 E35 A36 R37 R43 G58 A59 S60 W61 H63 V219 V249 P250 G266 W424 A433 Y434 G462 E463 G471 C472 A473 A476
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H67
Catalytic site (residue number reindexed from 1) H63
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:3cnt, PDBe:3cnt, PDBj:3cnt
PDBsum3cnt
PubMed
UniProtP50264|FMS1_YEAST Polyamine oxidase FMS1 (Gene Name=FMS1)

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