Structure of PDB 7wtd Chain D Binding Site BS03

Receptor Information
>7wtd Chain D (length=1145) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YKPIKKVMVANRGEIAIRVFRACTELGIRTVAIYSEQDTGQMHRQKADEA
YLIGRGLAPVQAYLHIPDIIKVAKENNVDAVHPGYGFLSERADFAQACQD
AGVRFIGPSPEVVRKMGDKVEARAIAIAAGVPVVPGTDAPITSLHEAHEF
SNTYGFPIIFKAAYGGGGRGMRVVHSYEELEENYTRAYSEALAAFGNGAL
FVEKFIEKPRHIEVQILGDQYGNILHLYERDCSIQRRHQKVVEIAPAAHL
DPQLRTRLTSDSVKLAKQVGYENAGTVEFLVDRHGKHYFIEVNSRLQVEH
TVTEEITDVDLVHAQIHVAEGRSLPDLGLRQENIRINGCAIQCRVTTEDP
ARSFQPDTGRIEVFRSGEGMGIRLDNASAFQGAVISPHYDSLLVKVIAHG
KDHPTAATKMSRALAEFRVRGVKTNIAFLQNVLNNQQFLAGTVDTQFIDE
NPELFQLRPAQNRAQKLLHYLGHVMVNGPTTPIPVKASPSPTDPVVPAVP
IGPPPAGFRDILLREGPEGFARAVRNHPGLLLMDTTFRDAHQSLLATRVR
THDLKKIAPYVAHNFSKLFSMENWGGATFDVAMRFLYECPWRRLQELREL
IPNIPFQMLLRGANAVGYTNYPDNVVFKFCEVAKENGMDVFRVFDSLNYL
PNMLLGMEAAGSAGGVVEAAISYTGDVADPSRTKYSLQYYMGLAEELVRA
GTHILCIKDMAGLLKPTACTMLVSSLRDRFPDLPLHIHTHDTSGAGVAAM
LACAQAGADVVDVAADSMSGMTSQPSMGALVACTRGTPLDTEVPMERVFD
YSEYWEGARGLYAAFDCTATMKSGNSDVYENEIPGGQYTNLHFQAHSMGL
GSKFKEVKKAYVEANQMLGDLIKVTPSSKIVGDLAQFMVQNGLSRAEAEA
QAEELSFPRSVVEFLQGYIGVPHGGFPEPFRSKVLKDLPRVEGRPGASLP
PLDLQALEKELVDRHGEEVTPEDVLSAAMYPDVFAHFKDFTATFGPLDSL
NTRLFLQGPKIAEEFEVELERGKTLHIKALAVSDLNRAGQRQVFFELNGQ
LRSILVKDTQAMKEMHFHPKALKDVKGQIGAPMPGKVIDIKVVAGAKVAK
GQPLCVLSAMKMETVVTSPMEGTVRKVHVTKDMTLEGDDLILEIE
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7wtd Chain D Residue 2002 [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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PDB7wtd Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		G199 M204 F238 I239 Q268 H271
Binding residue
(residue number reindexed from 1)		G166 M171 F205 I206 Q235 H238
Annotation score5
Enzymatic activity
Enzyme Commision number 6.4.1.1: pyruvate carboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004736 pyruvate carboxylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0009374 biotin binding
GO:0016874 ligase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006090 pyruvate metabolic process
GO:0006094 gluconeogenesis
GO:0006629 lipid metabolic process
GO:0006734 NADH metabolic process
GO:0006739 NADP metabolic process
GO:0010629 negative regulation of gene expression
GO:0019074 viral RNA genome packaging
GO:0019076 viral release from host cell
GO:0044794 positive regulation by host of viral process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7wtd, PDBe:7wtd, PDBj:7wtd
PDBsum7wtd
PubMed36283412
UniProtP11498|PYC_HUMAN Pyruvate carboxylase, mitochondrial (Gene Name=PC)

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