Structure of PDB 4ycl Chain A Binding Site BS01

Receptor Information

>4ycl Chain A (length=994) Species: 9986 (Oryctolagus cuniculus)

MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLW
ELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIA
NAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDI
VEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAV
NQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQ
QKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAV
ALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICS
DKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDK
PIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVE
KMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSP
AKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIK
EWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML
DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVAD
RAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAM
TGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEG
RAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTD
GLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVG
AAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMA
LSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYV
DPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Ligand information

• Ligand ID: CZA
• InChI: InChI=1S/C20H20N2O3/c1-9(23)14-18(24)17-16-11-8-21-13-6-4-5-10(15(11)13)7-12(16)20(2,3)22(17)19(14)25/h4-6,8,12,16-17,21,25H,7H2,1-3H3/t12-,16+,17+/m1/s1
• InChIKey: RLOAZVAJNNPPDI-DQYPLSBCSA-N
• SMILES:
  ACDLabs 10.04: O=C4C(C(=O)C)=C(O)N5C(C3Cc2c1c(cnc1ccc2)C3C45)(C)C
  CACTVS 3.341: CC(=O)C1=C(O)N2[C@@H]([C@@H]3[C@@H](Cc4cccc5[nH]cc3c45)C2(C)C)C1=O
  CACTVS 3.341: CC(=O)C1=C(O)N2[CH]([CH]3[CH](Cc4cccc5[nH]cc3c45)C2(C)C)C1=O
  OpenEye OEToolkits 1.5.0: CC(=O)C1=C(N2C(C1=O)C3c4c[nH]c5c4c(ccc5)CC3C2(C)C)O
  OpenEye OEToolkits 1.5.0: CC(=O)C1=C(N2[C@H](C1=O)[C@H]3c4c[nH]c5c4c(ccc5)C[C@H]3C2(C)C)O
• Formula: C20 H20 N2 O3
• Name: (6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE
• ChEMBL: CHEMBL260580
• DrugBank: DB07604
• PDB chain: 4ycl Chain A Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ycl Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): L61 V62 L98 N101 A102 L311
• Binding residue (residue number reindexed from 1): L61 V62 L98 N101 A102 L311
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.15,Kd=7nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D351 D703 D707
• Catalytic site (residue number reindexed from 1): D351 D703 D707
• Enzyme Commision number: 7.2.2.10: P-type Ca(2+) transporter.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005215 transporter activity
• GO:0005388 P-type calcium transporter activity
• GO:0005509 calcium ion binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006816 calcium ion transport
• GO:0006874 intracellular calcium ion homeostasis
• GO:0031448 positive regulation of fast-twitch skeletal muscle fiber contraction
• GO:0070588 calcium ion transmembrane transport
• GO:0106134 positive regulation of cardiac muscle cell contraction
• GO:1901896 positive regulation of ATPase-coupled calcium transmembrane transporter activity
• GO:1902082 positive regulation of calcium ion import into sarcoplasmic reticulum
• GO:1990036 calcium ion import into sarcoplasmic reticulum

Cellular Component

• GO:0016020 membrane
• GO:0016529 sarcoplasmic reticulum
• GO:0033017 sarcoplasmic reticulum membrane

External links

• PDB: RCSB:4ycl, PDBe:4ycl, PDBj:4ycl
• PDBsum: 4ycl
• PubMed: 17389383
• UniProt: P04191|AT2A1_RABIT Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (Gene Name=ATP2A1)