Structure of PDB 4yry Chain A Binding Site BS02

Receptor Information
>4yry Chain A (length=276) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGGTALNEIVKKVKIAEDVFDFWIHSPSVSKEARPGQFVVIRLHEKGERI
PLTVADTKPEEGLFRMVVKVVGKTTHELSLKKEGDTILDVVGPLGNPSEI
ENYGNVLLVGGGVGIATLYPIAKALKEAGNNITTVLGARTKDYLIMVDEF
KEISDVLLVTDDGSAGMKGVVTDAMDKLFRERKFDICWAVGPTIMMKFCT
LKAREFGVPIWVSLNPIMVDGTGMCGACRVTVSGQIKFACVDGPEFRGEE
VDWDELLKRLAQYREQEKISYERFLK
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 chain4yry Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yry Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		F38 E48 P51 L52 T53 V67 V68 K69 V71 G72 T74 T75 N215 P216 M218 Q266
Binding residue
(residue number reindexed from 1)		F38 E48 P51 L52 T53 V67 V68 K69 V71 G72 T74 T75 N215 P216 M218 Q266
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0051537 2 iron, 2 sulfur cluster binding
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:4yry, PDBe:4yry, PDBj:4yry
PDBsum4yry
PubMed26139605
UniProtQ9X1X4|PYRKH_THEMA Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog (Gene Name=TM_1639)

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