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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:

4bid

2.800 Å

X-ray

2013-04-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitogen-activated protein kinase kinase kinase 5
ID:M3K5_HUMAN
AC:Q99683
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.25


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:70.378
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.409864.000

% Hydrophobic% Polar
56.6443.36
According to VolSite

Ligand :
4bid_2 Structure
HET Code: IE8
Formula: C24H21N4O2
Molecular weight: 397.449 g/mol
DrugBank ID: -
Buried Surface Area:71.76 %
Polar Surface area: 91.58 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 5
Aromatic rings: 5
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-49.424212.5597-7.3576


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
C15CD1LEU- 6863.880Hydrophobic
C21CBLEU- 6863.930Hydrophobic
C9CG2VAL- 6944.050Hydrophobic
C17CG1VAL- 6944.260Hydrophobic
C19CG2VAL- 6943.780Hydrophobic
C17CBALA- 7074.030Hydrophobic
N2OGLU- 7552.87158.28H-Bond
(Ligand Donor)
N3NVAL- 7573.13166.99H-Bond
(Protein Donor)
C17CD1LEU- 8103.470Hydrophobic
C23CD2LEU- 8103.460Hydrophobic
C10CBSER- 8214.080Hydrophobic
NOD2ASP- 8223.870Ionic
(Ligand Cationic)
C2CBASP- 8224.420Hydrophobic