Structure of PDB 5rvy Chain A Binding Site BS01

Receptor Information
>5rvy Chain A (length=867) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DHGLARLVTVYCEHGHKAAKINPLFTGQALLENVPEIQALVQTLQGPFHT
AGLLNMGKEEASLEEVLVYLNQIYCGQISIETSQLQSQDEKDWFAKRFEE
LQKETFTTEERKHLSKLMLESQEFDHFLATKFSTVKRYGGEGAESMMGFF
HELLKMSAYSGITDVIIGMPHRGRLNLLTGLLQFPPELMFRKMRGLSEFP
ENFSATGDVLSHLTSSVDLYFGAHHPLHVTMLPNPSHLEAVNPVAVGKTR
GRQQSRQDGDYSPDNSAQPGDRVICLQVHGDASFCGQGIVPETFTLSNLP
HFRIGGSVHLIVNNQLGYTTPAERGRSSLYCSDIGKLVGCAIIHVNGDSP
EEVVRATRLAFEYQRQFRKDVIIDLLCYRQWGHNELDEPFYTNPIMYKII
RARKSIPDTYAEHLIAGGLMTQEEVSEIKSSYYAKLNDHLNNMAHYRPPA
LNLQAHWQGLAQPEAQITTWSTGVPLDLLRFVGMKSVEVPRELQMHSHLL
KTHVQSRMEKMMDGIKLDWATAEALALGSLLAQGFNVRLSGQDVGRGTFS
QRHAIVVCQETDDTYIPLNHMDPNQKGFLEVSNSPLSEEAVLGFEYGMSI
ESPKLLPLWEAQFGDFFNGAQIIFDTFISGGEAKWLLQSGIVILLPHGYD
GAGPDHSSCRIERFLQMCDSAEEGVDGDTVNMFVVHPTTPAQYFHLLRRQ
MVRNFRKPLIVASPKMLLRLPAAVSTLQEMAPGTTFNPVIGDSSVDPKKV
KTLVFCSGKHFYSLVKQRESLGAKKHDFAIIRVEELCPFPLDSLQQEMSK
YKHVKDHIWSQEEPQNMGPWSFVSPRFEKQLACKLRLVGRPPLPVPAVGI
GTVHLHQHEDILAKTFA
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain5rvy Chain A Residue 1001 [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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PDB5rvy PanDDA analysis group deposition
Resolution1.609 Å
Binding residue
(original residue number in PDB)		H223 R224 S288 H289 L290 G332 D333 A334 S335 Q339 N366 L368 G369 H435
Binding residue
(residue number reindexed from 1)		H171 R172 S236 H237 L238 G280 D281 A282 S283 Q287 N314 L316 G317 H383
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.4.-
Gene Ontology
Molecular Function
GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0030976 thiamine pyrophosphate binding
GO:0160166 2-oxoadipate dehydrogenase activity
Biological Process
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006091 generation of precursor metabolites and energy
GO:0006096 glycolytic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0160167 oxoadipate dehydrogenase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5rvy, PDBe:5rvy, PDBj:5rvy
PDBsum5rvy
PubMed
UniProtQ96HY7|DHTK1_HUMAN 2-oxoadipate dehydrogenase complex component E1 (Gene Name=DHTKD1)

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