Structure of PDB 1ep3 Chain B Binding Site BS01

Receptor Information
>1ep3 Chain B (length=261) Species: 1358 (Lactococcus lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQLQEMMTVVSQREVAYNIFEMVLKGTLVDEMDLPGQFLHLAVPNGAMLL
RRPISISSWDKRAKTCTILYRIGDETTGTYKLSKLESGAKVDVMGPLGNG
FPVAEVTSTDKILIIGGGIGVPPLYELAKQLEKTGCQMTILLGFASENVK
ILENEFSNLKNVTLKIATDDGSYGTKGHVGMLMNEIDFEVDALYTCGAPA
MLKAVAKKYDQLERLYISMESRMACGIGACYACVEHDKEDESHALKVCED
GPVFLGKQLSL
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 chain1ep3 Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ep3 Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L51 R53 P54 I55 S56 L70 Y71 T78 G79 T80 I120 E221 S222 R223
Binding residue
(residue number reindexed from 1)		L50 R52 P53 I54 S55 L69 Y70 T77 G78 T79 I119 E220 S221 R222
Annotation score4
Enzymatic activity
Enzyme Commision number 1.3.3.1: Transferred entry: 1.3.98.1.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0009055 electron transfer activity
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
GO:0044205 'de novo' UMP biosynthetic 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:1ep3, PDBe:1ep3, PDBj:1ep3
PDBsum1ep3
PubMed11188687
UniProtP56968|PYRK_LACLM Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit (Gene Name=pyrK)

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