Structure of PDB 6ph9 Chain A Binding Site BS03

Receptor Information
>6ph9 Chain A (length=243) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVATLFIADLHLQTEEPAITAGFLRFLQGEARQADALYILGDLFEAWIGD
DDPNPLHQQIASAIKAVVDAGVPCYFIHGNRDFLVGQRFARQSGMILLAE
EERLDLYGREVLIMHGDTLCTDDQGYLAFRAKVHTPWIQRLFLALPLFIR
HRIAARMRADSKAANSSKSMEIMDVNPQAVVDAMERHHVQWLIHGHTHRP
AVHELQANGQPAWRVVLGAWHSEGSMVKVTPDDVELIHFPFLE
Ligand information
Ligand IDLP5
InChIInChI=1S/C34H66NO12P/c1-3-5-7-9-11-13-15-17-19-21-26(37)23-29(39)35-31-33(32(41)28(25-36)45-34(31)47-48(42,43)44)46-30(40)24-27(38)22-20-18-16-14-12-10-8-6-4-2/h26-28,31-34,36-38,41H,3-25H2,1-2H3,(H,35,39)(H2,42,43,44)/t26-,27-,28-,31-,32-,33-,34-/m1/s1
InChIKeyHEHQDWUWJVPREQ-XQJZMFRCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCC[C@@H](O)CC(=O)N[C@H]1[C@H](O[C@H](CO)[C@@H](O)[C@@H]1OC(=O)C[C@H](O)CCCCCCCCCCC)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O
ACDLabs 10.04O=P(OC1OC(C(O)C(OC(=O)CC(O)CCCCCCCCCCC)C1NC(=O)CC(O)CCCCCCCCCCC)CO)(O)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(CC(=O)NC1C(C(C(OC1OP(=O)(O)O)CO)O)OC(=O)CC(CCCCCCCCCCC)O)O
CACTVS 3.341CCCCCCCCCCC[CH](O)CC(=O)N[CH]1[CH](O[CH](CO)[CH](O)[CH]1OC(=O)C[CH](O)CCCCCCCCCCC)O[P](O)(O)=O
FormulaC34 H66 N O12 P
Name(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
ChEMBL
DrugBank
ZINCZINC000058650130
PDB chain6ph9 Chain A Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ph9 Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		N79 R80 F82 L83 Y125 F128 F141 M156 R157 S160 N164 K167 H195
Binding residue
(residue number reindexed from 1)		N80 R81 F83 L84 Y126 F129 F142 M157 R158 S161 N165 K168 H196
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.1.54: UDP-2,3-diacylglucosamine diphosphatase.
Gene Ontology
Molecular Function
GO:0008758 UDP-2,3-diacylglucosamine hydrolase activity
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0019897 extrinsic component of plasma membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ph9, PDBe:6ph9, PDBj:6ph9
PDBsum6ph9
PubMed32041866
UniProtA6T5R0|LPXH_KLEP7 UDP-2,3-diacylglucosamine hydrolase (Gene Name=lpxH)

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