Structure of PDB 7ykn Chain A Binding Site BS02

Receptor Information
>7ykn Chain A (length=507) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYSVVRLILGDQLNHAHSWFSEHRDDVLYLIAELHQEQEYVRHHIQKQCA
FFAAMQAFADYLSAEGHHVWHLDLDASAQYNDLPDLIAQICQQVQADAFQ
YQRPDEYRLLEQMANLRLSGITIGCVDTEHFLLPFAEIPEQFPASKAVLM
EHFYRRMRKRFGYLMTADGKPEGGQWNFDADNRNKLKSPDLLQLPTPLCF
DNPVASIKARIERHRIPSIGQVGESLLWPINRAQALSLLAHFCQICLPNF
GRFQDAMTAQHPHRWSLYHSRLSFALNSKLLSPREVIEATISAYRAAQGQ
ISLAQVEGFVRQILGWREYVRGMYWSNMPHYQTRNHLGAQRPLPSYFWNG
QTKMRCLQQAITQSLDFGYAHHIQRLMVTGNFALLTECDPDQVDAWYLGI
YIDAIEWVELPNTRGMALFADGGLIATKPYSASGSYINKMSDYCASCAYQ
VKLKSGEKACPLNSLYWRFMLKHRDRMLYKTWDKMTSDSQQAILSTADAY
LSQIESL
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 chain7ykn Chain A Residue 604 [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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PDB7ykn The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F251 H270 S271 R272 S274 F310 Q313 I314 R318 Y370 H373 R376 L377 Y398 D404 A405 V409 E410 N413 T414
Binding residue
(residue number reindexed from 1)		F250 H269 S270 R271 S273 F309 Q312 I313 R317 Y369 H372 R375 L376 Y397 D403 A404 V408 E409 N412 T413
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:7ykn, PDBe:7ykn, PDBj:7ykn
PDBsum7ykn
PubMed36528063
UniProtA0A2V4NVF4

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