Structure of PDB 7ccz Chain B Binding Site BS01

Receptor Information
>7ccz Chain B (length=320) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSLFTKELEHALE
KNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLET
LPEKSVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQEFSAII
LATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGV
LHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLDG
SDSIQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRGPQLAAQNLGIS
LANLLLSKGAKNILDVARQL
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 chain7ccz Chain B 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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PDB7ccz Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Resolution1.79 Å
Binding residue
(original residue number in PDB)		S96 K98 D99 P101 T102 S146 S147 R149 R150 R173 L188 A189 V215 Q217 L254 C261 S262
Binding residue
(residue number reindexed from 1)		S60 K62 D63 P65 T66 S110 S111 R113 R114 R137 L151 A152 V178 Q180 L217 C224 S225
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 C224
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:7ccz, PDBe:7ccz, PDBj:7ccz
PDBsum7ccz
PubMed33600566
UniProtP08397|HEM3_HUMAN Porphobilinogen deaminase (Gene Name=HMBS)

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