PDB Entry (6sfe)
PDB ID: 6sfe Resolution: 1.08 Å Exp. Method: X-RAY DIFFRACTION
PMID: 32259333 DOI: 10.1002/chem.202000759
Protein
Protein Name: 3-dehydroquinate dehydratase
Uniprot ID/ACC: P24670 (AROD_SALTI) Organism: Salmonella typhi
Gene Symbol: aroD Gene ID: -
Protein Class: LYASE
Ligand
Ligand Name:   [(1S,2S,3R,5S)-5-carboxy-1,2,3-trihydroxycyclohexyl]methanaminium
Canonical SMILES:   [NH3+]C[C@@]1(O)C[C@H](C[C@@H](O)[C@@H]1O)C(O)=O
Standard InChI:   InChI=1S/C8H15NO5/c9-3-8(14)2-4(7(12)13)1-5(10)6(8)11/h4-6,10-11,14H,1-3,9H2,(H,12,13)/p+1/t4-,5+,6-,8-/m0/s1
HET Code:   L9Z PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C8H16NO5+ Mol. Weight:   206.1023 logP:   -2.8242
HBD:   5 HBA:   4
#Rotatable Bonds:   2 TPSA:   125.63
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Aliphatic Subsititution LYS 170 A 11.08 6.62 Aminium Ion
Binding Affinity
-