Structure of PDB 4y9r Chain A Binding Site BS02

Receptor Information
>4y9r Chain A (length=608) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPVKESSFVEKMKKTGRNIIVFYGSQTGTAEEFANRLSKDAHRYGMRGMS
ADPEEYDLADLSSLPEIDKSLVVFCMATYEGDPTDNAQDFYDWLQETDVD
LTGVKFAVFGLGNKTYEHFNAMGKYVDQRLEQLGAQRIFELGLGDDDGNL
EEDFITWREQFWPAVCEFFGVEATSSIRQYELVVHEDMDVAKVYTGEMGR
LKSYENQKPPFDAKNPFLAAVTANRKLNQGTERHLMHLELDISDSKIRYE
SGDHVAVYPANDSALVNQIGEILGADLDVIMSLNNLDEESNKKHPFPCPT
TYRTALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKEL
YLSWVVEARRHILAILQDYPSLRPPIDHLCELLPRLQARYYSIASSSKVH
PNSVHICAVAVEYEAKSGRVNKGVATSWLRAKEPARALVPMFVRKSQFRL
PFKSTTPVIMVGPGTGIAPFMGFIQERAWLREQGKEVGETLLYYGCRRSD
EDYLYREELARFHKDGALTQLNVAFSREQAHKVYVQHLLKRDREHLWKLI
HEGGAHIYVCGDARNMAKDVQNTFYDIVAEFGPMEHTQAVDYVKKLMTKG
RYSLDVWS
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 chain4y9r Chain A Residue 702 [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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PDB4y9r Mutants of Cytochrome P450 Reductase Lacking Either Gly-141 or Gly-143 Destabilize Its FMN Semiquinone.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H319 R454 Y455 Y456 S457 C472 A473 V476 Y478 G488 V489 A490 T491 W677
Binding residue
(residue number reindexed from 1)		H254 R389 Y390 Y391 S392 C407 A408 V411 Y413 G423 V424 A425 T426 W607
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y456 S457 C630 D675 W677
Catalytic site (residue number reindexed from 1) Y391 S392 C560 D605 W607
Enzyme Commision number 1.6.2.4: NADPH--hemoprotein reductase.
Gene Ontology
Molecular Function
GO:0003958 NADPH-hemoprotein reductase activity
GO:0004128 cytochrome-b5 reductase activity, acting on NAD(P)H
GO:0008941 nitric oxide dioxygenase NAD(P)H activity
GO:0009055 electron transfer activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0016787 hydrolase activity
GO:0019899 enzyme binding
GO:0047726 iron-cytochrome-c reductase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0050661 NADP binding
Biological Process
GO:0003420 regulation of growth plate cartilage chondrocyte proliferation
GO:0007584 response to nutrient
GO:0009410 response to xenobiotic stimulus
GO:0009437 carnitine metabolic process
GO:0009725 response to hormone
GO:0009812 flavonoid metabolic process
GO:0019395 fatty acid oxidation
GO:0022900 electron transport chain
GO:0032332 positive regulation of chondrocyte differentiation
GO:0043066 negative regulation of apoptotic process
GO:0043602 nitrate catabolic process
GO:0045542 positive regulation of cholesterol biosynthetic process
GO:0045880 positive regulation of smoothened signaling pathway
GO:0046210 nitric oxide catabolic process
GO:0070988 demethylation
GO:0071371 cellular response to gonadotropin stimulus
GO:0071372 cellular response to follicle-stimulating hormone stimulus
GO:0071375 cellular response to peptide hormone stimulus
GO:0071548 response to dexamethasone
GO:0090031 positive regulation of steroid hormone biosynthetic process
GO:0090181 regulation of cholesterol metabolic process
GO:0090346 cellular organofluorine metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4y9r, PDBe:4y9r, PDBj:4y9r
PDBsum4y9r
PubMed27189945
UniProtP00388|NCPR_RAT NADPH--cytochrome P450 reductase (Gene Name=Por)

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