Structure of PDB 3ies Chain A Binding Site BS01

Receptor Information
>3ies Chain A (length=431) Species: 7054 (Photinus pyralis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNIT
YAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAV
APANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIM
DSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSLPKG
VALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLI
CGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFFAKSTLIDKYDLS
NLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDD
KPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEA
TNALIDKDGWLHSGDIAYWDEDEHFFIVDRL
Ligand information
Ligand IDM24
InChIInChI=1S/C25H21FN7O9P/c26-15-7-2-1-6-14(15)23-31-21(32-41-23)12-4-3-5-13(8-12)25(36)42-43(37,38)39-9-16-18(34)19(35)24(40-16)33-11-30-17-20(27)28-10-29-22(17)33/h1-8,10-11,16,18-19,24,34-35H,9H2,(H,37,38)(H2,27,28,29)/t16-,18-,19-,24-/m1/s1
InChIKeyXGTSAMZIYGBAIU-VEBYGKHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(c(c1)c2nc(no2)c3cccc(c3)C(=O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)F
ACDLabs 11.02O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OC(=O)c4cccc(c4)c5nc(on5)c6ccccc6F
OpenEye OEToolkits 1.7.0c1ccc(c(c1)c2nc(no2)c3cccc(c3)C(=O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)F
CACTVS 3.352Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC(=O)c4cccc(c4)c5noc(n5)c6ccccc6F)[CH](O)[CH]3O
CACTVS 3.352Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)c4cccc(c4)c5noc(n5)c6ccccc6F)[C@@H](O)[C@H]3O
FormulaC25 H21 F N7 O9 P
Name5'-O-[(R)-[({3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]phenyl}carbonyl)oxy](hydroxy)phosphoryl]adenosine
ChEMBL
DrugBank
ZINCZINC000038142076
PDB chain3ies Chain A Residue 552 [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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PDB3ies Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H245 F247 G315 G316 A317 P318 G339 Y340 G341 L342 T343 S347 A348 V362 D422
Binding residue
(residue number reindexed from 1)		H238 F240 G308 G309 A310 P311 G332 Y333 G334 L335 T336 S340 A341 V355 D415
Annotation score2
Binding affinityMOAD: Kd~120pM
PDBbind-CN: -logKd/Ki=9.92,Kd=120pM
Enzymatic activity
Catalytic site (original residue number in PDB) S198 R218 H245 T343 E344
Catalytic site (residue number reindexed from 1) S196 R211 H238 T336 E337
Enzyme Commision number 1.13.12.7: firefly luciferase.
Gene Ontology
Molecular Function
GO:0004467 long-chain fatty acid-CoA ligase activity
GO:0004497 monooxygenase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
GO:0047077 Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity
GO:0051087 protein-folding chaperone binding
Biological Process
GO:0001676 long-chain fatty acid metabolic process
GO:0008218 bioluminescence
GO:0046949 fatty-acyl-CoA biosynthetic process
Cellular Component
GO:0005777 peroxisome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ies, PDBe:3ies, PDBj:3ies
PDBsum3ies
PubMed20194791
UniProtP08659|LUCI_PHOPY Luciferin 4-monooxygenase

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