Structure of PDB 5okd Chain D Binding Site BS01

Receptor Information
>5okd Chain D (length=239) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHL
VGVCYTEDEAKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAA
RAANNGALPPDLSYIVRARHGGEDYVFSLLTGYCEPPTGVSLREGLYFNP
YFPGQAIGMAPPIYNEVLEFDDGTPATMSQVAKDVCTFLRWAAEPEHDHR
KRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP
Ligand information
Ligand IDHEC
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKeyHXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
FormulaC34 H34 Fe N4 O4
NameHEME C
ChEMBL
DrugBank
ZINC
PDB chain5okd Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5okd X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		C37 C40 H41 N105 P111 R120 Y126 L131 F153 I158 G159 M160 P163
Binding residue
(residue number reindexed from 1)		C36 C39 H40 N104 P110 R119 Y125 L130 F152 I157 G158 M159 P162
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.8: quinol--cytochrome-c reductase.
Gene Ontology
Molecular Function
GO:0008121 ubiquinol-cytochrome-c reductase activity
GO:0009055 electron transfer activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0045275 respiratory chain complex III

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5okd, PDBe:5okd, PDBj:5okd
PDBsum5okd
PubMed29765610
UniProtP00125|CY1_BOVIN Cytochrome c1, heme protein, mitochondrial (Gene Name=CYC1)

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