Structure of PDB 2ekg Chain B Binding Site BS01

Receptor Information
>2ekg Chain B (length=299) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYFQGHMNLDLAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEA
LKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPK
YISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATL
RLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPK
EVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGI
PRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAER
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 chain2ekg Chain B Residue 2002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ekg Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine
Resolution1.9 Å
Binding residue
(original residue number in PDB)		X99 D133 M134 Q163 R184 V186 K187 G188 A189 A225 T226 H227 D228 Q252 V257 Y275
Binding residue
(residue number reindexed from 1)		X105 D139 M140 Q169 R190 V192 K193 G194 A195 A231 T232 H233 D234 Q258 V263 Y281
Annotation score1
Enzymatic activity
Enzyme Commision number 1.5.5.2: proline dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004657 proline dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0042803 protein homodimerization activity
GO:0071949 FAD binding
Biological Process
GO:0006560 proline metabolic process
GO:0006562 proline catabolic process
GO:0010133 proline catabolic process to glutamate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ekg, PDBe:2ekg, PDBj:2ekg
PDBsum2ekg
PubMed18426222
UniProtQ72IB8|PRODH_THET2 Proline dehydrogenase (Gene Name=TT_C1214)

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