Structure of PDB 3vrd Chain B Binding Site BS02

Receptor Information
>3vrd Chain B (length=400) Species: 1050 (Thermochromatium tepidum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEPNETYYTCYMSNEVIGG
DRELASLRVGYDGLRAHGIQVVHDSALGIDPDKKLVKTAGGAEFAYDRCV
VAPGIDLLYDKIEGYSEALAAKLPHAWKAGEQTALLRRQLESMDDGGVVI
IAPPAPPFRCPPGPYERASQIAHYLKAHKSKSKVIILDNSQTFSKQAQFT
KGWERLYGFGTENALIEWHPGPDAAVVKTDTEAMTVETSFGETFKAAVIN
LIPPQRAGKIAQSASLTNDSGWCPVDIRTFESSLQPGIHVIGDACNAAPM
PKSAYSANSQAKVAAAAVVALLKGEEPGTPSYLNTCYSILAPGYGISIAA
VYRPNAEGKAIEAVPDSGGITPVDAPDWVLEREVQYAHSWYNNIVHDTFG
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 chain3vrd Chain B Residue 501 [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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PDB3vrd Structure Analysis and Comparative Characterization of the Cytochrome c' and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum
Resolution1.5 Å
Binding residue
(original residue number in PDB)		V8 G9 G11 T12 G13 I33 E34 P35 Y39 C42 Y43 A77 A103 P104 G105 W128 R160 C161 G293 D294 K303 S304 A305 W391
Binding residue
(residue number reindexed from 1)		V7 G8 G10 T11 G12 I32 E33 P34 Y38 C41 Y42 A76 A102 P103 G104 W127 R159 C160 G292 D293 K302 S303 A304 W390
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding

View graph for
Molecular Function
External links
PDB RCSB:3vrd, PDBe:3vrd, PDBj:3vrd
PDBsum3vrd
PubMed22827326
UniProtD0G7Q4

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