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Structure of PDB 1c9h Chain A Binding Site BS01

Receptor Information

>1c9h Chain A (length=107) Species: 9606 (Homo sapiens)

GVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRI
GKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFD
VELLNLE

Ligand information

• Ligand ID: RAP
• InChI: InChI=1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33-,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1
• InChIKey: QFJCIRLUMZQUOT-HPLJOQBZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@@H]1CC[C@H]2C[C@@H](C(=CC=C\C=C\[C@H](C[C@H](C(=O)[C@@H]([C@@H](/C(=C/[C@H](C(=O)C[C@H](OC(=O)[C@@H]3CCCCN3C(=O)C(=O)[C@@]1(O2)O)[C@H](C)C[C@@H]4CC[C@H]([C@@H](C4)OC)O)C)/C)O)OC)C)C)C)OC
  CACTVS 3.341: CO[CH]1C[CH](CC[CH]1O)C[CH](C)[CH]2CC(=O)[CH](C)C=C(C)[CH](O)[CH](OC)C(=O)[CH](C)C[CH](C)C=CC=CC=C(C)[CH](C[CH]3CC[CH](C)[C](O)(O3)C(=O)C(=O)N4CCCC[CH]4C(=O)O2)OC
  ACDLabs 10.04: O=C2C(C)CC(C=CC=CC=C(C)C(OC)CC4OC(O)(C(=O)C(=O)N3C(C(=O)OC(C(C)CC1CCC(O)C(OC)C1)CC(=O)C(C=C(C)C(O)C2OC)C)CCCC3)C(CC4)C)C
  OpenEye OEToolkits 1.5.0: CC1CCC2CC(C(=CC=CC=CC(CC(C(=O)C(C(C(=CC(C(=O)CC(OC(=O)C3CCCCN3C(=O)C(=O)C1(O2)O)C(C)CC4CCC(C(C4)OC)O)C)C)O)OC)C)C)C)OC
  CACTVS 3.341: CO[C@@H]1C[C@@H](CC[C@H]1O)C[C@@H](C)[C@@H]2CC(=O)[C@H](C)/C=C(C)/[C@@H](O)[C@@H](OC)C(=O)[C@H](C)C[C@H](C)/C=C/C=C/C=C(C)/[C@H](C[C@@H]3CC[C@@H](C)[C@@](O)(O3)C(=O)C(=O)N4CCCC[C@H]4C(=O)O2)OC
• Formula: C51 H79 N O13
• Name: RAPAMYCIN IMMUNOSUPPRESSANT DRUG
• ChEMBL: CHEMBL413
• DrugBank: DB00877
• ZINC: ZINC000169289388
• PDB chain: 1c9h Chain A Residue 108

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1c9h Structure of FKBP12.6 in complex with rapamycin.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y26 F36 D37 F46 Q53 E54 V55 I56 F59 Y82 H87
• Binding residue (residue number reindexed from 1): Y26 F36 D37 F46 Q53 E54 V55 I56 F59 Y82 H87
• Annotation score: 1
• Binding affinity: BindingDB: Kd=0.200000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): Y26 F36 D37 I56 Y82 F99
• Catalytic site (residue number reindexed from 1): Y26 F36 D37 I56 Y82 F99
• Enzyme Commision number: 5.2.1.8: peptidylprolyl isomerase.

Gene Ontology

Molecular Function

• GO:0003755 peptidyl-prolyl cis-trans isomerase activity
• GO:0005102 signaling receptor binding
• GO:0005219 ryanodine-sensitive calcium-release channel activity
• GO:0005515 protein binding
• GO:0005528 FK506 binding
• GO:0016247 channel regulator activity
• GO:0019855 calcium channel inhibitor activity
• GO:0030551 cyclic nucleotide binding
• GO:0044325 transmembrane transporter binding

Biological Process

• GO:0002027 regulation of heart rate
• GO:0006458 'de novo' protein folding
• GO:0006939 smooth muscle contraction
• GO:0007204 positive regulation of cytosolic calcium ion concentration
• GO:0009749 response to glucose
• GO:0010459 negative regulation of heart rate
• GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
• GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
• GO:0019227 neuronal action potential propagation
• GO:0019722 calcium-mediated signaling
• GO:0022417 protein maturation by protein folding
• GO:0030073 insulin secretion
• GO:0033197 response to vitamin E
• GO:0035773 insulin secretion involved in cellular response to glucose stimulus
• GO:0042026 protein refolding
• GO:0042098 T cell proliferation
• GO:0042542 response to hydrogen peroxide
• GO:0048680 positive regulation of axon regeneration
• GO:0050849 negative regulation of calcium-mediated signaling
• GO:0051209 release of sequestered calcium ion into cytosol
• GO:0051280 negative regulation of release of sequestered calcium ion into cytosol
• GO:0051284 positive regulation of sequestering of calcium ion
• GO:0051775 response to redox state
• GO:0060314 regulation of ryanodine-sensitive calcium-release channel activity
• GO:0061179 negative regulation of insulin secretion involved in cellular response to glucose stimulus

Cellular Component

• GO:0005737 cytoplasm
• GO:0016020 membrane
• GO:0016529 sarcoplasmic reticulum
• GO:0030018 Z disc
• GO:0033017 sarcoplasmic reticulum membrane
• GO:0034704 calcium channel complex

External links

• PDB: RCSB:1c9h, PDBe:1c9h, PDBj:1c9h
• PDBsum: 1c9h
• PubMed: 10713512
• UniProt: P68106|FKB1B_HUMAN Peptidyl-prolyl cis-trans isomerase FKBP1B (Gene Name=FKBP1B)

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