Structure of PDB 5df5 Chain D Binding Site BS01

Receptor Information
>5df5 Chain D (length=104) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDVEKGKKIFVQKCAQCHTVEKGGKHKEGPNLHGLFGRKTGQAAGFSYTD
ANKNKGITWGEDTLMEYLENPKKYIPGTKMIFAGIKKKGERADLIAYLKK
ATNE
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 chain5df5 Chain D Residue 201 [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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PDB5df5 Phosphomimetic substitution of cytochrome C tyrosine 48 decreases respiration and binding to cardiolipin and abolishes ability to trigger downstream caspase activation.
Resolution1.301 Å
Binding residue
(original residue number in PDB)		K13 C14 C17 H18 E28 G29 P30 G41 Y48 T49 N52 W59 Y67 L68 T78 K79 M80 F82
Binding residue
(residue number reindexed from 1)		K13 C14 C17 H18 E28 G29 P30 G41 Y48 T49 N52 W59 Y67 L68 T78 K79 M80 F82
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0002931 response to ischemia
GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c
GO:0006123 mitochondrial electron transport, cytochrome c to oxygen
GO:0006915 apoptotic process
GO:0006979 response to oxidative stress
GO:0009629 response to gravity
GO:0010730 negative regulation of hydrogen peroxide biosynthetic process
GO:0034349 glial cell apoptotic process
GO:0034465 response to carbon monoxide
GO:0042743 hydrogen peroxide metabolic process
GO:0046688 response to copper ion
GO:1901857 positive regulation of cellular respiration
Cellular Component
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0005829 cytosol
GO:0043293 apoptosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5df5, PDBe:5df5, PDBj:5df5
PDBsum5df5
PubMed
UniProtP62898|CYC_RAT Cytochrome c, somatic (Gene Name=Cycs)

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