Structure of PDB 1dgf Chain B Binding Site BS01

Receptor Information
>1dgf Chain B (length=497) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RDPASDQMQHWKEQRAAQKADVLTTGAGNPVGDKLNVITVGPRGPLLVQD
VVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITKYSKAKVFEHIG
KKTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFF
IRDPILFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRG
IPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLS
QEDPDYGIRDLFNAIATGKYPSWTFYIQVMTFNQAETFPFNPFDLTKVWP
HKDYPLIPVGKLVLNRNPVNYFAEVEQIAFDPSNMPPGIEASPDKMLQGR
LFAYPDTHRHRLGPNYLHIPVNCPYRARVANYQRDGPMCMQDNQGGAPNY
YPNSFGAPEQQPSALEHSIQYSGEVRRFNTANDDNVTQVRAFYVNVLNEE
QRKRLCENIAGHLKDAQIFIQKKAVKNFTEVHPDYGSHIQALLDKYN
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 chain1dgf Chain B Residue 3001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1dgf Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		R72 V74 H75 R112 V146 G147 N148 P158 F161 S217 F334 M350 R354 Y358 T361 H362 R365
Binding residue
(residue number reindexed from 1)		R68 V70 H71 R108 V142 G143 N144 P154 F157 S213 F330 M346 R350 Y354 T357 H358 R361
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H75 N148 D335
Catalytic site (residue number reindexed from 1) H71 N144 D331
Enzyme Commision number 1.11.1.6: catalase.
Gene Ontology
Molecular Function
GO:0004046 aminoacylase activity
GO:0004096 catalase activity
GO:0004601 peroxidase activity
GO:0016209 antioxidant activity
GO:0016684 oxidoreductase activity, acting on peroxide as acceptor
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050661 NADP binding
Biological Process
GO:0000302 response to reactive oxygen species
GO:0001649 osteoblast differentiation
GO:0001657 ureteric bud development
GO:0001666 response to hypoxia
GO:0001822 kidney development
GO:0006641 triglyceride metabolic process
GO:0006979 response to oxidative stress
GO:0008203 cholesterol metabolic process
GO:0009060 aerobic respiration
GO:0009410 response to xenobiotic stimulus
GO:0009411 response to UV
GO:0009636 response to toxic substance
GO:0009642 response to light intensity
GO:0009650 UV protection
GO:0010193 response to ozone
GO:0010288 response to lead ion
GO:0014823 response to activity
GO:0014854 response to inactivity
GO:0020027 hemoglobin metabolic process
GO:0032355 response to estradiol
GO:0032868 response to insulin
GO:0033189 response to vitamin A
GO:0033197 response to vitamin E
GO:0033591 response to L-ascorbic acid
GO:0042542 response to hydrogen peroxide
GO:0042744 hydrogen peroxide catabolic process
GO:0043066 negative regulation of apoptotic process
GO:0045471 response to ethanol
GO:0046686 response to cadmium ion
GO:0051781 positive regulation of cell division
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0055093 response to hyperoxia
GO:0061692 cellular detoxification of hydrogen peroxide
GO:0070542 response to fatty acid
GO:0071363 cellular response to growth factor stimulus
GO:0072722 response to amitrole
GO:0080184 response to phenylpropanoid
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005778 peroxisomal membrane
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0032991 protein-containing complex
GO:0034774 secretory granule lumen
GO:0043231 intracellular membrane-bounded organelle
GO:0062151 catalase complex
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1dgf, PDBe:1dgf, PDBj:1dgf
PDBsum1dgf
PubMed10656833
UniProtP04040|CATA_HUMAN Catalase (Gene Name=CAT)

[Back to BioLiP]