Structure of PDB 5m6r Chain A Binding Site BS01

Receptor Information
>5m6r Chain A (length=340) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSTTGDKILDTA
LSKIGEKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRE
NPHDAVVFHPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKFPHLEFRSIR
GNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQ
GALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSVPVAV
HTAMKDGQLYLTGGVWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVG
ITARNIPRGPQLAAQNLGISLANLLLSKGAKNILDVARQL
Ligand information
Ligand ID7J8
InChIInChI=1S/C40H46N4O16/c1-18-23(10-37(53)54)20(3-7-34(47)48)28(42-18)15-31-26(13-40(59)60)22(5-9-36(51)52)30(44-31)16-32-25(12-39(57)58)21(4-8-35(49)50)29(43-32)14-27-24(11-38(55)56)19(17-41-27)2-6-33(45)46/h17,41-44H,2-16H2,1H3,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
InChIKeyVHZWMEJYGVBAFI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1[nH]c(Cc2[nH]c(Cc3[nH]c(Cc4[nH]cc(CCC(O)=O)c4CC(O)=O)c(CCC(O)=O)c3CC(O)=O)c(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O
OpenEye OEToolkits 2.0.6Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c[nH]4)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
FormulaC40 H46 N4 O16
Name3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5m6r 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

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PDB5m6r Structural basis of pyrrole polymerization in human porphobilinogen deaminase.
Resolution2.73 Å
Binding residue
(original residue number in PDB)		E73 S96 K98 D99 P101 T102 S146 S147 R149 R150 R173 A189 V215 Q217 L254 C261 S262
Binding residue
(residue number reindexed from 1)		E56 S79 K81 D82 P84 T85 S129 S130 R132 R133 R156 A172 V198 Q200 L237 C244 S245
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) K81 D82 R132 R133 R150 R156 C244
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:5m6r, PDBe:5m6r, PDBj:5m6r
PDBsum5m6r
PubMed29908816
UniProtP08397|HEM3_HUMAN Porphobilinogen deaminase (Gene Name=HMBS)

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