Structure of PDB 7w3o Chain D Binding Site BS01

Receptor Information
>7w3o Chain D (length=270) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAITLESPDIKYPLRLIDREIISHDTRRFRFALPSPQHILGLPVGQHIYL
SARIDGNLVVRPYTPISSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYL
ESMQIGDTIEFRGPSGLLVYQGKGKFAIRPDKKSNPIIRTVKSVGMIAGG
TGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLRPELEELRNKHSA
RFKLWYTLDRAPEAWDYGQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQ
YACLPNLDHVGHPTERCFVF
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 chain7w3o Chain D Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7w3o The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3.
Resolution2.46 Å
Binding residue
(original residue number in PDB)		R66 P67 Y68 T69 V83 I84 Y87 F95 G98 G99 K100 M101 S102 T156 T159 P160
Binding residue
(residue number reindexed from 1)		R61 P62 Y63 T64 V78 I79 Y82 F90 G93 G94 K95 M96 S97 T151 T154 P155
Annotation score2
Enzymatic activity
Enzyme Commision number 1.6.2.2: cytochrome-b5 reductase.
Gene Ontology
Molecular Function
GO:0004128 cytochrome-b5 reductase activity, acting on NAD(P)H
GO:0005515 protein binding
GO:0016208 AMP binding
GO:0016491 oxidoreductase activity
GO:0043531 ADP binding
GO:0050421 nitrite reductase (NO-forming) activity
GO:0050660 flavin adenine dinucleotide binding
GO:0051287 NAD binding
GO:0071949 FAD binding
Biological Process
GO:0006695 cholesterol biosynthetic process
GO:0006809 nitric oxide biosynthetic process
GO:0008015 blood circulation
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005811 lipid droplet
GO:0005833 hemoglobin complex
GO:0016020 membrane
GO:0031966 mitochondrial membrane
GO:0035578 azurophil granule lumen
GO:1903958 nitric-oxide synthase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7w3o, PDBe:7w3o, PDBj:7w3o
PDBsum7w3o
PubMed36543799
UniProtP00387|NB5R3_HUMAN NADH-cytochrome b5 reductase 3 (Gene Name=CYB5R3)

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