Structure of PDB 5oeq Chain B Binding Site BS01

Receptor Information
>5oeq Chain B (length=417) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGL
GRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAAL
PFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADG
EIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVT
ASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQL
PAKLRSEPLKFDIGELWYRKSGTYRGKVQNLTQFYHGFLQYQFVIPTEAV
DEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKD
GLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKV
DPLRVFASDMARRLELL
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 chain5oeq Chain B Residue 900 [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]
PDB5oeq Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes.
Resolution2.25 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)		W10 A47 G49 L50 G51 R52 S53 Y54 N57 A58 P110 G111 T112 V115 T116 G118 G119 A122 C123 I125 H126 N172 G173 I178 Y371
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5oeq, PDBe:5oeq, PDBj:5oeq
PDBsum5oeq
PubMed28815830
UniProtP9WJF1|DPRE1_MYCTU Decaprenylphosphoryl-beta-D-ribose oxidase (Gene Name=dprE1)

[Back to BioLiP]