Structure of PDB 5jwc Chain A Binding Site BS01

Receptor Information
>5jwc Chain A (length=495) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKEKIIILGSGWGGFNFLLNIDFKKYDVTLISPRNYFTFTPLLPCLCSGT
LSVNVCTESIRNFLRKKNGYCGNYLQLECTDVFYEDKYINCIDIENNKVK
LFYDYLIIAVGAKTNTFNINGVDKYAYFVKDIDDALKIRKKFLDILEKCT
LPNISNEEKKKMLHVAVVGGGPTGVEVTAEFADFINKEVKINYKDIFNFI
SISIIEGGNNLLPTFTQNISDFTKENFHNLNINVLTNYYVIDVDKHSFHI
QSSLNKNEKKKLSYGLLIWASGLAQTTLIQKFLKTIPVQANNAILKVDEK
LRVIGIPSNNIYAIGDCKKIQPKLLHEHTNEIIKILTGNKLTSEALKLKQ
SELTKTFPQLSISKWDYEKNKKGEMTPQQFHDYLFEIDKNYKSPTPTAQN
AKQEAYYLSNVFNNFIHTNQKFNIPSFIEKWKGSLAYIGNHQVVADLPYY
ELKGGRFSSTFWKVVYIQLLLSWKSRFHFFIDFIKTKWYGRPFIK
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 chain5jwc Chain A Residue 601 [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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PDB5jwc Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria
Resolution2.051 Å
Binding residue
(original residue number in PDB)		G47 S48 G49 W50 G51 S70 P71 R72 T78 P79 C117 A147 V148 G149 V167 T211 G353 D354 P434 T435 A436
Binding residue
(residue number reindexed from 1)		G9 S10 G11 W12 G13 S32 P33 R34 T40 P41 C79 A109 V110 G111 V129 T173 G315 D316 P396 T397 A398
Annotation score2
Enzymatic activity
Enzyme Commision number 1.6.5.9: NADH:ubiquinone reductase (non-electrogenic).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003954 NADH dehydrogenase activity
GO:0003960 NADPH:quinone reductase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050136 NADH:ubiquinone reductase (non-electrogenic) activity
Biological Process
GO:0006116 NADH oxidation
Cellular Component
GO:0005739 mitochondrion

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5jwc, PDBe:5jwc, PDBj:5jwc
PDBsum5jwc
PubMed28195463
UniProtQ8I302

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