Structure of PDB 6hf3 Chain A Binding Site BS02

Receptor Information
>6hf3 Chain A (length=427) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGRGAIARGLGR
SYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPF
GLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEI
RHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTAS
LDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPA
KLRSEPLKFDANKYTFGPIGELWYRKSGTYRGKVQNLTQFYHPLPAGFLQ
YQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGW
NICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRV
DEWISVRRKVDPLRVFASDMARRLELL
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain6hf3 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hf3 Novel insight into the reaction of nitro, nitroso and hydroxylamino benzothiazinones and of benzoxacinones with Mycobacterium tuberculosis DprE1.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		W16 A53 G55 L56 G57 R58 S59 Y60 N63 A64 P116 G117 T118 V121 T122 G124 G125 A128 C129 I131 H132 N178 I183 I184 Y415 K418
Binding residue
(residue number reindexed from 1)		W10 A45 G47 L48 G49 R50 S51 Y52 N55 A56 P108 G109 T110 V113 T114 G116 G117 A120 C121 I123 H124 N170 I175 I176 Y381 K384
Annotation score3
Enzymatic activity
Enzyme Commision number 1.1.98.3: decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase.
Gene Ontology
Molecular Function
GO:0003885 D-arabinono-1,4-lactone oxidase activity
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0035884 arabinan biosynthetic process
GO:0045227 capsule polysaccharide biosynthetic process
GO:0046677 response to antibiotic
GO:0070592 cell wall polysaccharide biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0042597 periplasmic space

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6hf3, PDBe:6hf3, PDBj:6hf3
PDBsum6hf3
PubMed30194385
UniProtP9WJF1|DPRE1_MYCTU Decaprenylphosphoryl-beta-D-ribose oxidase (Gene Name=dprE1)

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