Structure of PDB 3nam Chain A Binding Site BS02

Receptor Information

>3nam 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: OTK
• InChI: InChI=1S/C26H38O10/c1-8-10-19(28)34-18-12-24(6,36-15(5)27)16-11-17(33-22(29)13(3)9-2)14(4)20(16)21-26(18,32)25(7,31)23(30)35-21/h9,14,16-18,20-21,31-32H,8,10-12H2,1-7H3/b13-9-/t14-,16-,17+,18-,20+,21-,24-,25+,26+/m0/s1
• InChIKey: INROUDCDOCKFKL-SBRSFKGSSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CCCC(=O)OC1CC(C2CC(C(C2C3C1(C(C(=O)O3)(C)O)O)C)OC(=O)C(=CC)C)(C)OC(=O)C
  ACDLabs 12.01: O=C3OC2C1C(C)C(OC(=O)\C(=C/C)C)CC1C(OC(=O)C)(CC(OC(=O)CCC)C2(O)C3(O)C)C
  OpenEye OEToolkits 1.7.0: CCCC(=O)O[C@H]1C[C@]([C@H]2C[C@H]([C@@H]([C@H]2[C@H]3[C@]1([C@](C(=O)O3)(C)O)O)C)OC(=O)/C(=C\C)/C)(C)OC(=O)C
  CACTVS 3.370: CCCC(=O)O[CH]1C[C](C)(OC(C)=O)[CH]2C[CH](OC(=O)C(C)=CC)[CH](C)[CH]2[CH]3OC(=O)[C](C)(O)[C]13O
  CACTVS 3.370: CCCC(=O)O[C@H]1C[C@](C)(OC(C)=O)[C@H]2C[C@@H](OC(=O)\C(C)=C/C)[C@H](C)[C@H]2[C@@H]3OC(=O)[C@@](C)(O)[C@@]13O
• Formula: C26 H38 O10
• Name: (3S,3aR,4S,6S,6aS,8R,9R,9aR,9bS)-6-(acetyloxy)-4-(butanoyloxy)-3,3a-dihydroxy-3,6,9-trimethyl-2-oxododecahydroazuleno[4,5-b]furan-8-yl (2Z)-2-methylbut-2-enoate
• ChEMBL: CHEMBL372254
• ZINC: ZINC000028526508
• PDB chain: 3nam Chain A Residue 997

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nam Critical roles of hydrophobicity and orientation of side chains for inactivation of sarcoplasmic reticulum Ca2+-ATPase with thapsigargin and thapsigargin analogs
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): E255 F256 L260 V772 F834 Y837
• Binding residue (residue number reindexed from 1): E255 F256 L260 V772 F834 Y837
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.46,Kd=3.5nM

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:0005515 protein 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:0070588 calcium ion transmembrane transport

Cellular Component

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

External links

• PDB: RCSB:3nam, PDBe:3nam, PDBj:3nam
• PDBsum: 3nam
• PubMed: 20551329
• UniProt: B6CAM1