Structure of PDB 4p8t Chain A Binding Site BS01

Receptor Information
>4p8t Chain A (length=456) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARG
LGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAA
LPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTAD
GEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDV
TASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQ
LPAKLRSEPLKFDAPQLLTLPDVFPNGLANKYTFGPIGELWYRKSGTYRG
KVQNLTQFYHPLDMFGEWNRAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQ
ASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDR
RVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMA
RRLELL
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 chain4p8t Chain A 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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PDB4p8t 2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1.
Resolution2.55 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 G179 I184 Y415
Binding residue
(residue number reindexed from 1)		W11 A48 G50 L51 G52 R53 S54 Y55 N58 A59 P111 G112 T113 V116 T117 G119 G120 A123 C124 I126 H127 N173 G174 I179 Y410
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4p8t, PDBe:4p8t, PDBj:4p8t
PDBsum4p8t
PubMed25427196
UniProtP9WJF1|DPRE1_MYCTU Decaprenylphosphoryl-beta-D-ribose oxidase (Gene Name=dprE1)

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