Structure of PDB 5m7f Chain A Binding Site BS01

Receptor Information
>5m7f Chain A (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSSLFTKELEHALE
KNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLET
LPEKSVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAI
ILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDILDLVG
VLHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLD
GSDSIQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRGPQLAAQNLGI
SLANLLLSKGAKNILDV
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 chain5m7f Chain A Residue 401 [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]
PDB5m7f Structural basis of pyrrole polymerization in human porphobilinogen deaminase.
Resolution2.78 Å
Binding residue
(original residue number in PDB)		S96 K98 D99 S146 S147 R149 R173 A189 R195 Q217 C261
Binding residue
(residue number reindexed from 1)		S60 K62 D63 S110 S111 R113 R137 A153 R159 Q181 C225
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K98 D99 R149 R150 R167 R173 C261
Catalytic site (residue number reindexed from 1) K62 D63 R113 R114 R131 R137 C225
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m7f, PDBe:5m7f, PDBj:5m7f
PDBsum5m7f
PubMed29908816
UniProtP08397|HEM3_HUMAN Porphobilinogen deaminase (Gene Name=HMBS)

[Back to BioLiP]