Structure of PDB 6fdu Chain B Binding Site BS01

Receptor Information
>6fdu Chain B (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 IDD5W
InChIInChI=1S/C22H28Cl2N6O2/c1-5-13(2)19(21(31)27-12-17-6-7-26-18(11-25)28-17)29-22(32)20(30(3)4)14-8-15(23)10-16(24)9-14/h6-11,13,19-20,25H,5,12H2,1-4H3,(H,27,31)(H,29,32)/b25-11-/t13-,19-,20-/m0/s1
InChIKeyXBUAFLLXSYLZPV-BFFNQEOMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6[H]/N=C\c1nccc(n1)CNC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H](c2cc(cc(c2)Cl)Cl)N(C)C
CACTVS 3.385CC[CH](C)[CH](NC(=O)[CH](N(C)C)c1cc(Cl)cc(Cl)c1)C(=O)NCc2ccnc(C=N)n2
OpenEye OEToolkits 2.0.6CCC(C)C(C(=O)NCc1ccnc(n1)C=N)NC(=O)C(c2cc(cc(c2)Cl)Cl)N(C)C
CACTVS 3.385CC[C@H](C)[C@H](NC(=O)[C@@H](N(C)C)c1cc(Cl)cc(Cl)c1)C(=O)NCc2ccnc(C=N)n2
FormulaC22 H28 Cl2 N6 O2
Name(2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide
ChEMBL
DrugBank
ZINC
PDB chain6fdu Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6fdu Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D167 S168 W247 M262 A266 S274 W276 G342 C345
Binding residue
(residue number reindexed from 1)		D5 S6 W85 M100 A104 S112 W114 G180 C183
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.69,IC50=204uM
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:6fdu, PDBe:6fdu, PDBj:6fdu
PDBsum6fdu
PubMed30028574
UniProtB0B9A0|CDUB1_CHLT2 Deubiquitinase and deneddylase Dub1 (Gene Name=cdu1)

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