Structure of PDB 1np7 Chain B Binding Site BS01

Receptor Information
>1np7 Chain B (length=483) Species: 1148 (Synechocystis sp. PCC 6803) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKHVPPTVLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQ
GFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQIN
AKTIYYHREVTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDLPFSI
QDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPEFFP
QINFDHRSVLAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSS
KFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVA
QKYGNKLFNRGGLLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLT
GFMSNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTA
GIGNDARDFRYFNIPKQSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLS
ATEQKQWGVQLGVDYPRPCVNFHQSVEARRKIE
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 chain1np7 Chain B 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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PDB1np7 Identification of a new cryptochrome class: structure, function, and evolution
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y236 S249 S250 K251 S253 L256 E289 R293 F296 F352 N355 R358 Q359 F380 D386 Y387 D388 S391 N392 N395 W396
Binding residue
(residue number reindexed from 1)		Y236 S249 S250 K251 S253 L256 E289 R293 F296 F352 N355 R358 Q359 F380 D386 Y387 D388 S391 N392 N395 W396
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E289 W292 W320 N355 W373 W396
Catalytic site (residue number reindexed from 1) E289 W292 W320 N355 W373 W396
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003913 DNA photolyase activity
GO:0071949 FAD binding
GO:0097159 organic cyclic compound binding
Biological Process
GO:0000719 photoreactive repair
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
GO:0006950 response to stress

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1np7, PDBe:1np7, PDBj:1np7
PDBsum1np7
PubMed12535521
UniProtP77967|CRYD_SYNY3 Cryptochrome DASH (Gene Name=cry)

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