Structure of PDB 5k8k Chain A Binding Site BS03

Receptor Information
>5k8k Chain A (length=237) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKHSYFISDLHLSETQPELTALFVDFMQNLAPQAERLYILGDLFDFWIGD
DEQSALIQQVKDLIKFVSDQGVQCYFQHGNRDFLIGERFSKETGAQLLPD
YQLITLYDKKILLCHGDTLCIDDEAYQQFRRRVHQKWLQRLFLCLPLKVR
VIIAEKIRAKSNQDKQAKSQEIMDVNQAFTAEKVQEFGVNLLIHGHTHRE
AIHQQEEFTRIVLGDWRKNYASILKMDESGEFGFIKD
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 chain5k8k Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5k8k Structure of the essential Haemophilus influenzae UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		N80 R81 D123 Y126 F129 L138 Q139 F142 R158 K160 S161 D164 K165 K168 M173 H196 H198
Binding residue
(residue number reindexed from 1)		N80 R81 D123 Y126 F129 L138 Q139 F142 R158 K160 S161 D164 K165 K168 M173 H196 H198
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5k8k, PDBe:5k8k, PDBj:5k8k
PDBsum5k8k
PubMed27780190
UniProtP44046|LPXH_HAEIN UDP-2,3-diacylglucosamine hydrolase (Gene Name=lpxH)

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