Structure of PDB 2ybq Chain A Binding Site BS02

Receptor Information
>2ybq Chain A (length=242) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIALLP
ESCQRIYVGPQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELERLL
EAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQLDLDWAG
LARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQAGQQVTR
GALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLG
Ligand information
Ligand IDUP2
InChIInChI=1S/C40H44N4O16/c45-33(46)5-1-17-21(9-37(53)54)29-14-27-19(3-7-35(49)50)22(10-38(55)56)30(43-27)15-28-20(4-8-36(51)52)24(12-40(59)60)32(44-28)16-31-23(11-39(57)58)18(2-6-34(47)48)26(42-31)13-25(17)41-29/h41-44H,1-16H2,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
InChIKeyHUHWZXWWOFSFKF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC(=O)CCc1c2Cc3[nH]c(Cc4[nH]c(Cc5[nH]c(Cc([nH]2)c1CC(O)=O)c(CCC(O)=O)c5CC(O)=O)c(CCC(O)=O)c4CC(O)=O)c(CC(O)=O)c3CCC(O)=O
ACDLabs 12.01O=C(O)Cc1c(c5nc1Cc2nc(c(c2CCC(=O)O)CC(=O)O)Cc3c(c(c(n3)Cc4c(c(c(n4)C5)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O
OpenEye OEToolkits 1.7.0C1c2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c([nH]4)Cc5c(c(c1[nH]5)CCC(=O)O)CC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O
FormulaC40 H44 N4 O16
NameUROPORPHYRINOGEN III
ChEMBL
DrugBank
ZINCZINC000085545850
PDB chain2ybq Chain A Residue 1268 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ybq Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen III Methyltransferases.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R51 L52 F109 R111 H161 L162 Q163 M186 L188 G189 P241
Binding residue
(residue number reindexed from 1)		R39 L40 F89 R91 H141 L142 Q143 M162 L164 G165 P217
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D50 M186
Catalytic site (residue number reindexed from 1) D38 M162
Enzyme Commision number 2.1.1.107: uroporphyrinogen-III C-methyltransferase.
Gene Ontology
Molecular Function
GO:0004851 uroporphyrin-III C-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0009236 cobalamin biosynthetic process
GO:0019354 siroheme biosynthetic process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ybq, PDBe:2ybq, PDBj:2ybq
PDBsum2ybq
PubMed21632530
UniProtP95417

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