Structure of PDB 7wtd Chain D Binding Site BS02

Receptor Information

>7wtd Chain D (length=1145) Species: 9606 (Homo sapiens)

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 ID: COA
• InChI: InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
• InChIKey: RGJOEKWQDUBAIZ-IBOSZNHHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
  CACTVS 3.341: CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
  ACDLabs 10.04: O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
• Formula: C21 H36 N7 O16 P3 S
• Name: COENZYME A
• ChEMBL: CHEMBL1213327
• DrugBank: DB01992
• ZINC: ZINC000008551087
• PDB chain: 7wtd Chain D Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7wtd Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): R398 R445 R451 R453 Q494 R496 K1056
• Binding residue (residue number reindexed from 1): R365 R412 R418 R420 Q461 R463 K1023
• Annotation score: 2

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

External links

• PDB: RCSB:7wtd, PDBe:7wtd, PDBj:7wtd
• PDBsum: 7wtd
• PubMed: 36283412
• UniProt: P11498|PYC_HUMAN Pyruvate carboxylase, mitochondrial (Gene Name=PC)