Structure of PDB 6c0e Chain A Binding Site BS01

Receptor Information
>6c0e Chain A (length=419) Species: 272624 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMTYDKIKVPAQGEAITVAADHSLHVPDNPIIPFIEGDGIGVDVTPPMIR
VVDAAVQKAYGNKRKISWMEVYAGEKATKVYGGDQWLPKETLDAMKKYVV
SIKGPLTTPVGGGIRSLNVAIRQDMDLYVCLRPIRYFNGVPSPVREPWKT
DMVIFRENSEDIYAGIEWQADTPEAKKVIQFLTKEMGVKKIRFPEHCGIG
VKPVSREGTTRLVKAAIQYAIDNDRSTVTLVHKGNIMKFTEGAFKDWGYQ
VARDSFGAKEYQGGPWMEFKNPKTGKQIIINDVIADAFLQQILLRPEDYS
VIATLNLNGDYISDALAAQVGGIGIAPGANISDQMAVFEATHGTAPKYAG
QNKVNPGSIILSAEMMLRHMGWYEAADLIIRGMEGAIEAKTVTYDFERGM
QGATLVSSSGFADAMIKHM
Ligand information
Ligand IDEE1
InChIInChI=1S/C26H34N7O22P3/c27-21-15-23(30-7-29-21)33(8-31-15)25-20(54-56(43,44)45)18(38)13(53-25)6-51-58(48,49)55-57(46,47)50-5-12-17(37)19(39)24(52-12)32-2-1-9(11(4-32)22(28)40)10(3-14(34)35)16(36)26(41)42/h1-2,4,7-10,12-13,17-20,24-25,37-39H,3,5-6H2,(H2,28,40)(H,34,35)(H,41,42)(H,46,47)(H,48,49)(H2,27,29,30)(H2,43,44,45)/t9-,10-,12+,13+,17+,18+,19+,20+,24+,25+/m0/s1
InChIKeyWSGZIHXYYXDDDT-PJNAXEGASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CC(C(=C5)C(=O)N)C(CC(=O)O)C(=O)C(=O)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.385NC(=O)C1=CN(C=C[C@H]1[C@H](CC(O)=O)C(=O)C(O)=O)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=C[C@H](C(=C5)C(=O)N)[C@H](CC(=O)O)C(=O)C(=O)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.385NC(=O)C1=CN(C=C[CH]1[CH](CC(O)=O)C(=O)C(O)=O)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC26 H34 N7 O22 P3
Name(3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid;
NADPH with ketoglutarate adduct
ChEMBL
DrugBank
ZINC
PDB chain6c0e Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6c0e Crystal Structure of Isocitrate Dehydrogenase from Legionella pneumophila with bound NADPH with an ??-ketoglutarate adduct
Resolution1.7 Å
Binding residue
(original residue number in PDB)
P108 L109 T111 S119 N121 R125 R135 R159 D313 I326 E342 H345 G346 T347 A348 K350 Y351 V357 N358 Y397 D398
Binding residue
(residue number reindexed from 1)
P105 L106 T108 S116 N118 R122 R132 R156 D310 I323 E339 H342 G343 T344 A345 K347 Y348 V354 N355 Y394 D395
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Y166 K236 D289 D313
Catalytic site (residue number reindexed from 1) Y163 K233 D286 D310
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004450 isocitrate dehydrogenase (NADP+) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6c0e, PDBe:6c0e, PDBj:6c0e
PDBsum6c0e
PubMed
UniProtQ5ZXB6

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