Structure of PDB 5m1e Chain A Binding Site BS02

Receptor Information
>5m1e Chain A (length=469) Species: 199310 (Escherichia coli CFT073) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENP
KGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKKQVLNMPTK
RLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKER
QNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGA
DPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVL
EGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTG
RPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQ
YAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDP
ARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKK
DPDVVAHIDAIWDELAIFN
Ligand information
Ligand ID7D9
InChIInChI=1S/C22H31N4O12PS/c1-9-5-11-16-15(10(9)2)22(3,4)6-14(40(35,36)37)26(16)17-19(23-21(31)24-20(17)30)25(11)7-12(27)18(29)13(28)8-38-39(32,33)34/h5,12-14,18,27-29H,6-8H2,1-4H3,(H2,32,33,34)(H,35,36,37)(H2,23,24,30,31)/t12-,13+,14+,18-/m0/s1
InChIKeyTZDQUUMSMXVHAK-LWGWVAHUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc2c3c(c1C)C(CC(N3C4=C(N2CC(C(C(COP(=O)(O)O)O)O)O)NC(=O)NC4=O)S(=O)(=O)O)(C)C
OpenEye OEToolkits 2.0.6Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)NC(=O)NC4=O)S(=O)(=O)O)(C)C
CACTVS 3.385Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)C3=C(N4[CH](CC(C)(C)c(c1C)c24)[S](O)(=O)=O)C(=O)NC(=O)N3
CACTVS 3.385Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)C3=C(N4[C@@H](CC(C)(C)c(c1C)c24)[S](O)(=O)=O)C(=O)NC(=O)N3
FormulaC22 H31 N4 O12 P S
Name
ChEMBL
DrugBank
ZINCZINC000584905445
PDB chain5m1e Chain A Residue 502 [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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PDB5m1e Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
Resolution2.62 Å
Binding residue
(original residue number in PDB)		T160 N175 I178 Y179 R180 R192 L194 R197 V232 E241
Binding residue
(residue number reindexed from 1)		T137 N152 I155 Y156 R157 R169 L171 R174 V209 E218
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.98: 4-hydroxy-3-polyprenylbenzoate decarboxylase.
Gene Ontology
Molecular Function
GO:0008694 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
GO:0016831 carboxy-lyase activity
GO:0046872 metal ion binding
Biological Process
GO:0006744 ubiquinone biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m1e, PDBe:5m1e, PDBj:5m1e
PDBsum5m1e
PubMed28057757
UniProtP0AAB5|UBID_ECOL6 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (Gene Name=ubiD)

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