Structure of PDB 6fdq Chain A Binding Site BS01

Receptor Information
>6fdq Chain A (length=239) Species: 471472 (Chlamydia trachomatis L2/434/Bu) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPAWDSDIIFKCLCYFHTLYPGLIPLETFPPATIFNFKQKIISILEDKKA
VLRGEPIKGPLPICCSKENYRRHLQRTTLLPVFMWYHPTPKTLSDTMQTM
KQLAIKGSVGASHWLLVIVDIQARRLVYFDSLYNYVMPPENMKKELQSFA
QQLDQVYPAYDSKKFSVKIAAKEVIQRGSGSSCGAWCCQFLHWYLKDPLT
DALNDLPVDSVERHENLASFVQACEAAVQDLPELSWPEA
Ligand information
Ligand ID2UQ
InChIInChI=1S/C13H12N4O/c14-6-12-15-8-11(9-16-12)13(18)17-7-10-4-2-1-3-5-10/h1-6,8-9,14H,7H2,(H,17,18)/b14-6+
InChIKeyLOHVEJATQLMRBB-MKMNVTDBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2[H]/N=C/c1ncc(cn1)C(=O)NCc2ccccc2
CACTVS 3.385N=Cc1ncc(cn1)C(=O)NCc2ccccc2
OpenEye OEToolkits 1.9.2c1ccc(cc1)CNC(=O)c2cnc(nc2)C=N
ACDLabs 12.01O=C(c1cnc(nc1)C=[N@H])NCc2ccccc2
FormulaC13 H12 N4 O
NameN-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6fdq Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fdq Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		W247 M262 L265 A266 S270 V271 S274 W276 C345
Binding residue
(residue number reindexed from 1)		W85 M100 L103 A104 S108 V109 S112 W114 C183
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.95,IC50=113uM
Enzymatic activity
Enzyme Commision number 3.4.22.-
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:6fdq, PDBe:6fdq, PDBj:6fdq
PDBsum6fdq
PubMed30028574
UniProtB0B9A0|CDUB1_CHLT2 Deubiquitinase and deneddylase Dub1 (Gene Name=cdu1)

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