PDB Entry (6q7j)
PDB ID: 6q7j Resolution: 2.14 Å Exp. Method: X-RAY DIFFRACTION
PMID: 31263766 DOI: 10.1021/acscentsci.9b00221
Protein
Protein Name: Exo-1,4-beta-xylosidase xlnD
Uniprot ID/ACC: Q5BAS1 (XYND_EMENI) Organism: Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans)
Gene Symbol: xlnD Gene ID: 2875035
Protein Class: HYDROLASE
Ligand
Ligand Name:   3,3-dimethyl-1-[4-({8-[(1R,2S,3S,4S,5R,6S)-2,3,4,5-tetrahydroxy-7-azabicyclo[4.1.0]heptan-7-yl]octyl}carbamoyl)butyl]-2-[5-(1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene)penta-1,3-dien-1-yl]-3H-indol-1-ium
Canonical SMILES:   CN1\C(=C/C=C/C=C/C2=[N+](CCCCC(=O)NCCCCCCCC[N@@]3[C@H]4[C@@H]3[C@H](O)[C@H](O)[C@@H](O)[C@@H]4O)c3ccccc3C2(C)C)C(C)(C)c2ccccc12
Standard InChI:   InChI=1S/C45H62N4O5/c1-44(2)31-21-13-15-23-33(31)47(5)35(44)25-11-10-12-26-36-45(3,4)32-22-14-16-24-34(32)48(36)29-20-17-27-37(50)46-28-18-8-6-7-9-19-30-49-38-39(49)41(52)43(54)42(53)40(38)51/h10-16,21-26,38-43,51-54H,6-9,17-20,27-30H2,1-5H3/p+1/t38-,39+,40+,41-,42-,43-,49?/m0/s1
HET Code:   HLB PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C45H63N4O5+ Mol. Weight:   739.4793 logP:   5.6238
HBD:   5 HBA:   7
#Rotatable Bonds:   17 TPSA:   119.28
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Aziridine Opening ASP 307 A 14.5 - Aziridine
Binding Affinity
-