Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4nif

2.150 Å

X-ray

2013-11-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitogen-activated protein kinase 1
ID:MK01_HUMAN
AC:P28482
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.24


Chains:

Chain Name:Percentage of Residues
within binding site
D2 %
E98 %


Ligand binding site composition:

B-Factor:31.202
Number of residues:46
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 0
Water Molecules: 5
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.4371211.625

% Hydrophobic% Polar
45.1354.87
According to VolSite

Ligand :
4nif_2 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:71.01 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-35.894838.6088-50.1027


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
O2GNALA- 352.78162.41H-Bond
(Protein Donor)
O2BNTYR- 362.91154.02H-Bond
(Protein Donor)
O2BNGLY- 372.96146.43H-Bond
(Protein Donor)
C1'CG2VAL- 394.30Hydrophobic
C5'CG2VAL- 394.010Hydrophobic
O1BNZLYS- 542.82172.2H-Bond
(Protein Donor)
O1ANZLYS- 542.76149.59H-Bond
(Protein Donor)
O1BNZLYS- 542.820Ionic
(Protein Cationic)
O1ANZLYS- 542.760Ionic
(Protein Cationic)
N6OE1GLN- 1052.93169.98H-Bond
(Ligand Donor)
N6OASP- 1062.94168.04H-Bond
(Ligand Donor)
N1NMET- 1083.06161.92H-Bond
(Protein Donor)
O2'OD2ASP- 1112.61164.76H-Bond
(Ligand Donor)
O1GNZLYS- 1513.980Ionic
(Protein Cationic)
O3GNZLYS- 1512.690Ionic
(Protein Cationic)
O3GNZLYS- 1512.69168.77H-Bond
(Protein Donor)
O3'OSER- 1532.68145.12H-Bond
(Ligand Donor)
C2'CD2LEU- 1563.990Hydrophobic
N3BOD2ASP- 1673.44134.64H-Bond
(Ligand Donor)
N3BOD1ASP- 1672.84157.81H-Bond
(Ligand Donor)
O3GOHOH- 5102.72179.98H-Bond
(Protein Donor)