Structure of PDB 3eq1 Chain A Binding Site BS01

Receptor Information
>3eq1 Chain A (length=312) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAFTKELEHALEKNE
VDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPE
KSVVGTSSLRRAAQLQRKFPHLEFRSIQGNLNTRLRKLDEQQEFSAIILA
TAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLH
DPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLDGSD
SIQETMQATIHVPQHEDDPQLVGITARNIPRGPQLAAQNLGISLANLLLS
KGAKNILDVARQ
Ligand information
Ligand IDDPM
InChIInChI=1S/C20H24N2O8/c1-10-13(6-19(27)28)12(3-5-18(25)26)16(22-10)8-15-14(7-20(29)30)11(9-21-15)2-4-17(23)24/h9,21-22H,2-8H2,1H3,(H,23,24)(H,25,26)(H,27,28)(H,29,30)
InChIKeyLCAXMKQKEYTFDM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1[nH]c(Cc2[nH]cc(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O
OpenEye OEToolkits 1.7.6Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
ACDLabs 12.01O=C(O)Cc1c(ncc1CCC(=O)O)Cc2c(c(c(n2)C)CC(=O)O)CCC(=O)O
FormulaC20 H24 N2 O8
Name3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid;
DIPYRROMETHANE COFACTOR
ChEMBL
DrugBankDB04517
ZINCZINC000015277485
PDB chain3eq1 Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3eq1 Structure of human porphobilinogen deaminase at 2.8 A: the molecular basis of acute intermittent porphyria
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S96 K98 D99 S146 S147 R149 R150 R173 L188 A189 C261
Binding residue
(residue number reindexed from 1)		S57 K59 D60 S107 S108 R110 R111 R134 L149 A150 C222
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K98 D99 R149 R150 Q167 R173 C261
Catalytic site (residue number reindexed from 1) K59 D60 R110 R111 Q128 R134 C222
Enzyme Commision number 2.5.1.61: hydroxymethylbilane synthase.
Gene Ontology
Molecular Function
GO:0004418 hydroxymethylbilane synthase activity
GO:0005515 protein binding
GO:0016740 transferase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0006783 heme biosynthetic process
GO:0006784 heme A biosynthetic process
GO:0006785 heme B biosynthetic process
GO:0018160 peptidyl-pyrromethane cofactor linkage
GO:0033014 tetrapyrrole biosynthetic process
GO:0048034 heme O biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3eq1, PDBe:3eq1, PDBj:3eq1
PDBsum3eq1
PubMed19207107
UniProtP08397|HEM3_HUMAN Porphobilinogen deaminase (Gene Name=HMBS)

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