Structure of PDB 3r5w Chain A Binding Site BS01

Receptor Information
>3r5w Chain A (length=109) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIPVALLTTTGRKTGQPRVNPLYFLRDGGRVIVAASKGGAEKNPMWYLNL
KANPKVQVQIKKEVLDLTARDATDEERAEYWPQLVTMYPSYQDYQSWTDR
TIPIVVCEP
Ligand information
Ligand IDF42
InChIInChI=1S/C29H36N5O18P/c1-12(25(42)31-17(28(46)47)4-6-21(38)30-16(27(44)45)5-7-22(39)40)52-53(49,50)51-11-20(37)23(41)19(36)10-34-18-9-14(35)3-2-13(18)8-15-24(34)32-29(48)33-26(15)43/h2-3,8-9,12,16-17,19-20,23,35-37,41H,4-7,10-11H2,1H3,(H,30,38)(H,31,42)(H,39,40)(H,44,45)(H,46,47)(H,49,50)(H,33,43,48)/t12-,16-,17-,19-,20+,23-/m0/s1
InChIKeyGEHSZWRGPHDXJO-NALJQGANSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13)C(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.5C[C@@H](C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)O[P@](=O)(O)OC[C@H]([C@H]([C@H](CN1c2cc(ccc2C=C3C1=NC(=O)NC3=O)O)O)O)O
OpenEye OEToolkits 1.7.5CC(C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)OP(=O)(O)OCC(C(C(CN1c2cc(ccc2C=C3C1=NC(=O)NC3=O)O)O)O)O
CACTVS 3.385C[C@H](O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O
ACDLabs 10.04O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)C(OP(=O)(O)OCC(O)C(O)C(O)CN3c1c(ccc(O)c1)C=C2C3=NC(=O)NC2=O)C)CCC(=O)O
FormulaC29 H36 N5 O18 P
NameCOENZYME F420
ChEMBL
DrugBankDB03913
ZINCZINC000198210272
PDB chain3r5w Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3r5w Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.
Resolution1.786 Å
Binding residue
(original residue number in PDB)		G53 R54 K55 T56 R60 P63 L64 Y65 A76 A77 S78 K79 P86 M87 W88 N91
Binding residue
(residue number reindexed from 1)		G11 R12 K13 T14 R18 P21 L22 Y23 A34 A35 S36 K37 P44 M45 W46 N49
Annotation score1
Binding affinityMOAD: Kd=1uM
Enzymatic activity
Enzyme Commision number 1.-.-.-
1.1.98.-
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity

View graph for
Molecular Function
External links
PDB RCSB:3r5w, PDBe:3r5w, PDBj:3r5w
PDBsum3r5w
PubMed22244759
UniProtP9WP15|DDN_MYCTU Deazaflavin-dependent nitroreductase (Gene Name=ddn)

[Back to BioLiP]