Structure of PDB 4cdn Chain A Binding Site BS02

Receptor Information
>4cdn Chain A (length=463) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAK
EANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRG
DPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHN
VVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPELGMVET
LSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRL
DSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFL
DEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEE
FEAGKTHDPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIA
ICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCK
RKFDVKLYIEKYS
Ligand information
Ligand IDFO1
InChIInChI=1S/C16H17N3O7/c20-6-12(23)13(24)11(22)5-19-10-4-8(21)2-1-7(10)3-9-14(19)17-16(26)18-15(9)25/h1-4,11-13,20-24H,5-6H2,(H,18,25,26)/t11-,12+,13-/m0/s1
InChIKeyAUEILLWDYUBWCM-XQQFMLRXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc2c(cc1O)N(C3=NC(=O)NC(=O)C3=C2)C[C@@H]([C@@H]([C@@H](CO)O)O)O
ACDLabs 10.04O=C1C=3C(=NC(=O)N1)N(c2c(ccc(O)c2)C=3)CC(O)C(O)C(O)CO
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13
CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@@H](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13
OpenEye OEToolkits 1.5.0c1cc2c(cc1O)N(C3=NC(=O)NC(=O)C3=C2)CC(C(C(CO)O)O)O
FormulaC16 H17 N3 O7
Name1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol;
7,8-didemethyl-8-hydroxy-5-deazariboflavin
ChEMBL
DrugBank
ZINCZINC000100069844
PDB chain4cdn Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cdn Structural and Evolutionary Aspects of Antenna Chromophore Usage by Class II Photolyases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
S26 R27 F55 C56 L57 T58 F61 M72 S118 K123 H272 F273 R411
Binding residue
(residue number reindexed from 1)
S31 R32 F60 C61 L62 T63 F66 M77 S123 K128 H273 F274 R412
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E301 W305 A335 G375
Catalytic site (residue number reindexed from 1) E302 W306 A336 G376
Enzyme Commision number 4.1.99.3: deoxyribodipyrimidine photo-lyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003904 deoxyribodipyrimidine photo-lyase activity
GO:0016829 lyase activity
Biological Process
GO:0000719 photoreactive repair
GO:0006281 DNA repair

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4cdn, PDBe:4cdn, PDBj:4cdn
PDBsum4cdn
PubMed24849603
UniProtQ8PYK9

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