Structure of PDB 1nkm Chain A Binding Site BS01

Receptor Information
>1nkm Chain A (length=220) Species: 10359 (Human betaherpesvirus 5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQALPLNIN
HDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPV
SPLQPDKVVEFLSGSYAGLSLSSRRTTPFKHVALCSVGRRRGTLAVYGRD
PEWVTQRFPDLTAADRDGLRAQWQGDPFRSDSYGLLGNSVDALYIRERLP
KLRYDKQLVGVTERESYVKA
Ligand information
Ligand ID0FP
InChIInChI=1S/C37H63N7O7/c1-11-25(24-18-14-12-15-19-24)40-33(49)29(47)23(2)39-32(48)26(22-28(46)44(9)10)41-34(50)31(37(6,7)8)43-35(51)30(36(3,4)5)42-27(45)20-16-13-17-21-38/h12,14-15,18-19,23,25-26,29-31,47H,11,13,16-17,20-22,38H2,1-10H3,(H,39,48)(H,40,49)(H,41,50)(H,42,45)(H,43,51)/t23-,25+,26-,29-,30+,31+/m0/s1
InChIKeyRICYNZHPHSJRNO-GYZAPQSVSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC[C@@H](NC(=O)[C@@H](O)[C@H](C)NC(=O)[C@H](CC(=O)N(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCCN)C(C)(C)C)C(C)(C)C)c1ccccc1
OpenEye OEToolkits 1.7.0CCC(c1ccccc1)NC(=O)C(C(C)NC(=O)C(CC(=O)N(C)C)NC(=O)C(C(C)(C)C)NC(=O)C(C(C)(C)C)NC(=O)CCCCCN)O
ACDLabs 12.01O=C(NC(C(=O)NC(C(=O)NC(C(=O)NC(C)C(O)C(=O)NC(c1ccccc1)CC)CC(=O)N(C)C)C(C)(C)C)C(C)(C)C)CCCCCN
OpenEye OEToolkits 1.7.0CC[C@H](c1ccccc1)NC(=O)[C@H]([C@H](C)NC(=O)[C@H](CC(=O)N(C)C)NC(=O)[C@H](C(C)(C)C)NC(=O)[C@H](C(C)(C)C)NC(=O)CCCCCN)O
CACTVS 3.370CC[CH](NC(=O)[CH](O)[CH](C)NC(=O)[CH](CC(=O)N(C)C)NC(=O)[CH](NC(=O)[CH](NC(=O)CCCCCN)C(C)(C)C)C(C)(C)C)c1ccccc1
FormulaC37 H63 N7 O7
NameN-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide;
BILC 408
ChEMBL
DrugBank
ZINCZINC000098207801
PDB chain1nkm Chain A Residue 260 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1nkm Structural and Biochemical Studies of Inhibitor Binding to Human Cytomegalovirus Protease
Resolution2.7 Å
Binding residue
(original residue number in PDB)		N62 H63 S132 S134 S135 R136 K156 C161 G164 R165 I231
Binding residue
(residue number reindexed from 1)		N50 H51 S120 S122 S123 R124 K130 C135 G138 R139 I195
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,IC50<0.05uM
Enzymatic activity
Enzyme Commision number 3.4.21.97: assemblin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1nkm, PDBe:1nkm, PDBj:1nkm
PDBsum1nkm
PubMed12549906
UniProtP16753|SCAF_HCMVA Capsid scaffolding protein (Gene Name=UL80)

[Back to BioLiP]