Structure of PDB 6mp5 Chain B Binding Site BS01

Receptor Information
>6mp5 Chain B (length=413) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNHYEVLVLGGGSGGITMAARMKRKVGAENVAIVEPSERHFYQPIWTLVG
AGAKQLSSSGRPTASVIPSGVEWIKARVTELNPDKNCIHTDDDEKISYRY
LIIALGIQLDYEKIKGLPEGFAHPKIGSNYSVKTVEKTWKALQDFKEGNA
IFTFPNTPVKCAGAPQKIMYLSEAYFRKTGKRSKANIIFNTSLGAIFGVK
KYADALQEIIQERNLTVNYKKNLIEVRADKQEAVFENLDKPGETQVISYE
MLHVTPPMSPPDVLKTSPVADAAGWVDVDKETLQHRRYPNVFGIGDCTNL
PTSKTAAAVAAQSGILDRTISVIMKNQTPTKKYDGYTSCPLVTGYNRVIL
AEFDYKAEPLETFPFDQSKERLSMYLMKADLMPFLYWNMMLRGYWGGPAF
LRKLFHLGMSLEH
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 chain6mp5 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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PDB6mp5 X-Ray Structure of Human Sulfide:Quinone Oxidoreductase: Insights into the Mechanism of Mitochondrial Hydrogen Sulfide Oxidation.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		G52 S53 E75 P76 Q83 P84 R117 V118 L145 G146 Y170 C201 G335 D336 T345 A346 A347 V349
Binding residue
(residue number reindexed from 1)		G12 S13 E35 P36 Q43 P44 R77 V78 L105 G106 Y130 C161 G295 D296 T305 A306 A307 V309
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K173 C201 I389 E392 K418
Catalytic site (residue number reindexed from 1) K133 C161 I349 E352 K378
Enzyme Commision number 1.8.5.8: eukaryotic sulfide quinone oxidoreductase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0048038 quinone binding
GO:0070224 sulfide:quinone oxidoreductase activity
GO:0071949 FAD binding
GO:0106436 glutathione-dependent sulfide quinone oxidoreductase activity
Biological Process
GO:0070221 sulfide oxidation, using sulfide:quinone oxidoreductase
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6mp5, PDBe:6mp5, PDBj:6mp5
PDBsum6mp5
PubMed30905673
UniProtQ9Y6N5|SQOR_HUMAN Sulfide:quinone oxidoreductase, mitochondrial (Gene Name=SQOR)

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