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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3cgo

3.000 Å

X-ray

2008-03-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitogen-activated protein kinase 10
ID:MK10_HUMAN
AC:P53779
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.24


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:34.255
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.5031353.375

% Hydrophobic% Polar
50.6249.38
According to VolSite

Ligand :
3cgo_1 Structure
HET Code: JNO
Formula: C19H25N7O
Molecular weight: 367.448 g/mol
DrugBank ID: DB08026
Buried Surface Area:56.21 %
Polar Surface area: 89.9 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 4
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
23.368.2782231.1759


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C09CD1ILE- 703.770Hydrophobic
C10CBILE- 703.910Hydrophobic
C16CBALA- 913.970Hydrophobic
C16SDMET- 1463.770Hydrophobic
N12OMET- 1493.18158.8H-Bond
(Ligand Donor)
N18NMET- 1493.01161.42H-Bond
(Protein Donor)
C08CG1VAL- 1964.050Hydrophobic
C16CD2LEU- 2064.140Hydrophobic