Structure of PDB 3nan Chain A Binding Site BS01

Receptor Information

>3nan 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: HZ1
• InChI: InChI=1S/C51H77NO15/c1-11-13-14-15-19-24-39(56)63-43-41-40(32(4)42(43)64-45(57)31(3)12-2)44-51(61,50(10,60)46(58)65-44)37(30-49(41,9)66-33(5)53)62-38(55)25-21-22-34-26-27-36(54)35(29-34)23-18-16-17-20-28-52-47(59)67-48(6,7)8/h12,26-27,29,32,37,40-44,54,60-61H,11,13-25,28,30H2,1-10H3,(H,52,59)/b31-12-/t32-,37+,40?,41-,42+,43+,44+,49+,50-,51-/m1/s1
• InChIKey: MJLFQZMEQWPDGU-UKQHJVOGSA-N
• SMILES:
  ACDLabs 12.01: O=C(OC(C)(C)C)NCCCCCCc1c(O)ccc(c1)CCCC(=O)OC3CC(OC(=O)C)(C2C(OC(=O)CCCCCCC)C(OC(=O)\C(=C/C)C)C(C)C2C4OC(=O)C(O)(C)C34O)C
  OpenEye OEToolkits 1.7.0: CCCCCCCC(=O)O[C@H]1[C@H]2C([C@H]3[C@]([C@H](C[C@]2(C)OC(=O)C)OC(=O)CCCc4ccc(c(c4)CCCCCCNC(=O)OC(C)(C)C)O)([C@](C(=O)O3)(C)O)O)C([C@@H]1OC(=O)/C(=C\C)/C)C
  CACTVS 3.370: CCCCCCCC(=O)O[CH]1[CH](OC(=O)C(C)=CC)[CH](C)[CH]2[CH]3OC(=O)[C](C)(O)[C]3(O)[CH](C[C](C)(OC(C)=O)[CH]12)OC(=O)CCCc4ccc(O)c(CCCCCCNC(=O)OC(C)(C)C)c4
  CACTVS 3.370: CCCCCCCC(=O)O[C@@H]1[C@@H](OC(=O)\C(C)=C/C)[C@H](C)[C@@H]2[C@@H]3OC(=O)[C@@](C)(O)[C@@]3(O)[C@H](C[C@](C)(OC(C)=O)[C@@H]12)OC(=O)CCCc4ccc(O)c(CCCCCCNC(=O)OC(C)(C)C)c4
  OpenEye OEToolkits 1.7.0: CCCCCCCC(=O)OC1C2C(C(C1OC(=O)C(=CC)C)C)C3C(C(CC2(C)OC(=O)C)OC(=O)CCCc4ccc(c(c4)CCCCCCNC(=O)OC(C)(C)C)O)(C(C(=O)O3)(C)O)O
• Formula: C51 H77 N O15
• PDB chain: 3nan Chain A Residue 997

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nan 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): L253 E255 F256 Q259 L260 V263 I307 P308 E309 P312 I765 V772 V773 L828 I829 F834
• Binding residue (residue number reindexed from 1): L253 E255 F256 Q259 L260 V263 I307 P308 E309 P312 I765 V772 V773 L828 I829 F834
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.22,Kd=6nM

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:3nan, PDBe:3nan, PDBj:3nan
• PDBsum: 3nan
• PubMed: 20551329
• UniProt: B6CAM1