Structure of PDB 2dc3 Chain B Binding Site BS01

Receptor Information
>2dc3 Chain B (length=168) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPGEMEIERRERSEELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNF
PSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVS
SVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAK
LRGLIYSHVTAAYKEVGW
Ligand information
Ligand IDHEM
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,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain2dc3 Chain B Residue 191 [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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PDB2dc3 High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode.
Resolution1.68 Å
Binding residue
(original residue number in PDB)		A56 Y59 F60 Q77 H81 R84 V85 H113 H117 V119 F124 L127
Binding residue
(residue number reindexed from 1)		A53 Y56 F57 Q74 H78 R81 V82 H110 H114 V116 F121 L124
Annotation score1
Enzymatic activity
Enzyme Commision number 1.11.1.-
1.14.12.-
1.15.1.1: superoxide dismutase.
1.7.-.-
Gene Ontology
Molecular Function
GO:0004096 catalase activity
GO:0004601 peroxidase activity
GO:0004784 superoxide dismutase activity
GO:0005344 oxygen carrier activity
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0019825 oxygen binding
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0047888 fatty acid peroxidase activity
GO:0070025 carbon monoxide binding
GO:0098809 nitrite reductase activity
GO:0141118 nitric oxide dioxygenase activity, heme protein as donor
Biological Process
GO:0001666 response to hypoxia
GO:0006979 response to oxidative stress
GO:0010764 negative regulation of fibroblast migration
GO:0015671 oxygen transport
GO:0019395 fatty acid oxidation
GO:0019430 removal of superoxide radicals
GO:0032966 negative regulation of collagen biosynthetic process
GO:0046210 nitric oxide catabolic process
GO:2000490 negative regulation of hepatic stellate cell activation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043005 neuron projection
GO:0043025 neuronal cell body

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2dc3, PDBe:2dc3, PDBj:2dc3
PDBsum2dc3
PubMed16699195
UniProtQ8WWM9|CYGB_HUMAN Cytoglobin (Gene Name=CYGB)

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