Structure of PDB 8pf4 Chain D Binding Site BS02

Receptor Information
>8pf4 Chain D (length=491) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMSKAFDLVVIGAGSGGLEAGWNAATLYGKRVAVVDVQTSHGPPFYAA
LGGTCVNVGCVPKKLMVTGAQYMDHLRESAGFGWEFDGSSVKANWKKLIA
AKNEAVLDINKSYEGMFNDTEGLDFFLGWGSLESKNVVVVRETADPKSAV
KERLQADHILLATGSWPQMPAIPGIEHCISSNEAFYLPEPPRRVLTVGGG
FISVEFAGIFNAYKPPGGKVTLCYRNNLILRGFDETIREEVTKQLTANGI
EIMTNENPAKVSLNTDGSKHVTFESGKTLDVDVVMMAIGRIPRTNDLQLG
NVGVKLTPKGGVQVDEFSRTNVPNIYAIGDITDRLMLTPVAINEGAALVD
TVFGNKPRKTDHTRVASAVFSIPPIGTCGLIEEVAAKEFEKVAVYMSSFT
PLMHNISGSKYKKFVAKIVTNHSDGTVLGVHLLGDGAPEIIQAVGVCLRL
NAKISDFYNTIGVHPTSAEELCSMRTPSYYYVKGEKMEKLP
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 chain8pf4 Chain D Residue 502 [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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PDB8pf4 Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		I10 G11 G13 S14 G15 V34 D35 V36 A46 A47 G50 T51 C52 V55 G56 C57 K60 G127 T160 G161 F198 R287 R290 G326 D327 M333 L334 T335
Binding residue
(residue number reindexed from 1)		I13 G14 G16 S17 G18 V37 D38 V39 A49 A50 G53 T54 C55 V58 G59 C60 K63 G130 T163 G164 F201 R290 R293 G329 D330 M336 L337 T338
Annotation score2
Enzymatic activity
Enzyme Commision number 1.8.1.12: trypanothione-disulfide reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0015036 disulfide oxidoreductase activity
GO:0015042 trypanothione-disulfide reductase (NADPH) activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0045454 cell redox homeostasis
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0020015 glycosome
GO:0097014 ciliary plasm

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8pf4, PDBe:8pf4, PDBj:8pf4
PDBsum8pf4
PubMed38164929
UniProtQ389T8

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