Structure of PDB 1nmk Chain A Binding Site BS01

Receptor Information
>1nmk Chain A (length=165) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKG
SCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM
ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNG
KTSKKITIADCGQLE
Ligand information
Ligand IDSFM
InChIInChI=1S/C39H56N4O10/c1-23(2)34-37(50)40-31(22-27-11-9-12-28(46)21-27)38(51)43-19-10-13-30(42-43)39(52)53-33(24(3)18-20-44)15-8-6-7-14-32(47)26(5)35(48)29(36(49)41-34)17-16-25(4)45/h6-9,11-12,14,18,21,23,26,29-35,42,44,46-48H,10,13,15-17,19-20,22H2,1-5H3,(H,40,50)(H,41,49)/b8-6+,14-7+,24-18+/t26-,29+,30-,31-,32-,33-,34-,35+/m0/s1
InChIKeyWZVMDDRRINUPRQ-APBCKSDASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC1C(C=CC=CCC(OC(=O)C2CCCN(N2)C(=O)C(NC(=O)C(NC(=O)C(C1O)CCC(=O)C)C(C)C)Cc3cccc(c3)O)C(=CCO)C)O
CACTVS 3.370CC(C)[CH]1NC(=O)[CH](CCC(C)=O)[CH](O)[CH](C)[CH](O)C=CC=CC[CH](OC(=O)[CH]2CCC[N](N2)C(=O)[CH](Cc3cccc(O)c3)NC1=O)C(C)=CCO
ACDLabs 12.01O=C1OC(C(=C/CO)/C)CC=CC=CC(O)C(C)C(O)C(C(=O)NC(C(=O)NC(C(=O)N2NC1CCC2)Cc3cccc(O)c3)C(C)C)CCC(=O)C
OpenEye OEToolkits 1.7.0C[C@H]1[C@H](/C=C/C=C/C[C@H](OC(=O)[C@@H]2CCCN(N2)C(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H]([C@@H]1O)CCC(=O)C)C(C)C)Cc3cccc(c3)O)/C(=C/CO)/C)O
CACTVS 3.370CC(C)[C@@H]1NC(=O)[C@H](CCC(C)=O)[C@H](O)[C@@H](C)[C@@H](O)/C=C/C=C/C[C@H](OC(=O)[C@@H]2CCC[N@](N2)C(=O)[C@H](Cc3cccc(O)c3)NC1=O)\C(C)=C\CO
FormulaC39 H56 N4 O10
Name(13E,15E)-(3S,6S,9R,10R,11S,12S,18S,21S)-10,12-DIHYDROXY-3-(3-HYDROXYBEN-ZYL)-18-((E)-3-HYDROXY-1-METHYLPROPENYL)-6-ISOPROPYL-11-METHYL-9-(3-OXO-BUTYL)-19-OXA-1,4,7,25-TETRAAZA-BICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20-TETRAONE;
ANALOGUE OF MACROLIDE FROM DEGRADED SANGLIFEHRIN A
ChEMBL
DrugBank
ZINCZINC000098209398
PDB chain1nmk Chain A Residue 166 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1nmk Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure and Binding Data
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R55 F60 Q63 T73 A101 N102 Q111 F113 H126
Binding residue
(residue number reindexed from 1)		R55 F60 Q63 T73 A101 N102 Q111 F113 H126
Annotation score1
Binding affinityMOAD: ic50=5.7nM
PDBbind-CN: -logKd/Ki=8.24,IC50=5.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) R55 F60 Q63 N102 F113 L122 H126
Catalytic site (residue number reindexed from 1) R55 F60 Q63 N102 F113 L122 H126
Enzyme Commision number 5.2.1.8: peptidylprolyl isomerase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0016018 cyclosporin A binding
GO:0046790 virion binding
GO:0051082 unfolded protein binding
GO:1904399 heparan sulfate binding
Biological Process
GO:0000413 protein peptidyl-prolyl isomerization
GO:0001933 negative regulation of protein phosphorylation
GO:0001934 positive regulation of protein phosphorylation
GO:0006457 protein folding
GO:0006469 negative regulation of protein kinase activity
GO:0006915 apoptotic process
GO:0019076 viral release from host cell
GO:0030168 platelet activation
GO:0030182 neuron differentiation
GO:0030593 neutrophil chemotaxis
GO:0030595 leukocyte chemotaxis
GO:0032148 activation of protein kinase B activity
GO:0032873 negative regulation of stress-activated MAPK cascade
GO:0034389 lipid droplet organization
GO:0034599 cellular response to oxidative stress
GO:0042118 endothelial cell activation
GO:0043410 positive regulation of MAPK cascade
GO:0045069 regulation of viral genome replication
GO:0045070 positive regulation of viral genome replication
GO:0050714 positive regulation of protein secretion
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0060352 cell adhesion molecule production
GO:0061944 negative regulation of protein K48-linked ubiquitination
GO:0070527 platelet aggregation
GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:1903901 negative regulation of viral life cycle
GO:2001233 regulation of apoptotic signaling pathway
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0031982 vesicle
GO:0032991 protein-containing complex
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nmk, PDBe:1nmk, PDBj:1nmk
PDBsum1nmk
PubMed12656618
UniProtP62937|PPIA_HUMAN Peptidyl-prolyl cis-trans isomerase A (Gene Name=PPIA)

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