Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3zly

2.110 Å

X-ray

2013-02-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dual specificity mitogen-activated protein kinase kinase 1
ID:MP2K1_HUMAN
AC:Q02750
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.12.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:44.765
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.3301056.375

% Hydrophobic% Polar
52.4047.60
According to VolSite

Ligand :
3zly_1 Structure
HET Code: YSO
Formula: C8H6N4
Molecular weight: 158.160 g/mol
DrugBank ID: -
Buried Surface Area:72.2 %
Polar Surface area: 78.48 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
-19.795428.4332-2.88142


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C5CD1LEU- 744.460Hydrophobic
CABCG2VAL- 823.770Hydrophobic
CACCG1VAL- 823.960Hydrophobic
CAHCBALA- 953.580Hydrophobic
CADCEMET- 1433.670Hydrophobic
CALSDMET- 1433.420Hydrophobic
NAMOGLU- 1442.93148.25H-Bond
(Ligand Donor)
NAJNMET- 1462.97159.91H-Bond
(Protein Donor)
NAIOMET- 1463.26146.75H-Bond
(Ligand Donor)
CACCD2LEU- 1973.90Hydrophobic
CAHCD1LEU- 1973.340Hydrophobic
CADSGCYS- 2074.180Hydrophobic
NAIOHOH- 20173.48140.77H-Bond
(Ligand Donor)