Structure of PDB 3e12 Chain B Binding Site BS03

Receptor Information
>3e12 Chain B (length=256) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSI
HSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPA
FLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLT
ERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGGMREFIFPLI
RAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVAS
KYYETI
Ligand information
Ligand IDKD0
InChIInChI=1S/C8H15O11P/c9-3(1-4(10)8(14)15)6(12)7(13)5(11)2-19-20(16,17)18/h3,5-7,9,11-13H,1-2H2,(H,14,15)(H2,16,17,18)/t3-,5-,6-,7-/m1/s1
InChIKeyRTNBXJBOAIDPME-SHUUEZRQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(C(C(C(COP(=O)(O)O)O)O)O)O)C(=O)C(=O)O
CACTVS 3.341O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@H](O)CC(=O)C(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(O)C(O)CC(=O)C(=O)O
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O)C(=O)C(=O)O
CACTVS 3.341O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH](O)CC(=O)C(O)=O
FormulaC8 H15 O11 P
Name3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid
ChEMBL
DrugBank
ZINCZINC000003870009
PDB chain3e12 Chain B Residue 268 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3e12 Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		K41 K46 N48 R49 S50 Q99 K124 H185 D233
Binding residue
(residue number reindexed from 1)		K39 K44 N46 R47 S48 Q97 K122 H183 D225
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.99,Kd=1.02uM
Enzymatic activity
Enzyme Commision number 2.5.1.55: 3-deoxy-8-phosphooctulonate synthase.
Gene Ontology
Molecular Function
GO:0008676 3-deoxy-8-phosphooctulonate synthase activity
GO:0016740 transferase activity
Biological Process
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0019294 keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
GO:0046364 monosaccharide biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3e12, PDBe:3e12, PDBj:3e12
PDBsum3e12
PubMed19228070
UniProtO66496|KDSA_AQUAE 2-dehydro-3-deoxyphosphooctonate aldolase (Gene Name=kdsA)

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