Structure of PDB 2npx Chain A Binding Site BS01

Receptor Information
>2npx Chain A (length=447) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLSCGMQLYLEG
KVKDVNSVRYMTGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEER
VENYDKLIISPGAVPFELDIPGKDLDNIYLMRGRQWAIKLKQKTVDPEVN
NVVVIGSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEE
MEANNITIATGETVERYEGDGRVQKVVTDKNAYDADLVVVAVGVRPNTAW
LKGTLELHPNGLIKTDEYMRTSEPDVFAVGDATLIKYNPADTEVNIALAT
NARKQGRFAVKNLEEPVKPFPGVQGSSGLAVFDYKFASTGINEVMAQKLG
KETKAVTVVEDYLMDFNPDKQKAWFKLVYDPETTQILGAQLMSKADLTAN
INAISLAIQAKMTIEDLAYADFFFQPAFDKPWNIINTAALEAVKQER
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 chain2npx Chain A Residue 449 [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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PDB2npx NADH binding site and catalysis of NADH peroxidase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		L6 S9 H10 E32 K33 S41 C42 E78 I79 P111 G112 R132 I160 N247 G280 D281 A297 L298 A299
Binding residue
(residue number reindexed from 1)		L6 S9 H10 E32 K33 S41 C42 E78 I79 P111 G112 R132 I160 N247 G280 D281 A297 L298 A299
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H10 I37 S41 C42 K139 Q142 K143 R303 F423
Catalytic site (residue number reindexed from 1) H10 I37 S41 C42 K139 Q142 K143 R303 F423
Enzyme Commision number 1.11.1.1: NADH peroxidase.
Gene Ontology
Molecular Function
GO:0004601 peroxidase activity
GO:0016491 oxidoreductase activity
GO:0016692 NADH peroxidase activity
Biological Process
GO:0098869 cellular oxidant detoxification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2npx, PDBe:2npx, PDBj:2npx
PDBsum2npx
PubMed8425532
UniProtP37062|NAPE_ENTFA NADH peroxidase (Gene Name=npr)

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