scPDB - 3d83 entry

Protein Data Bank Entry:

PDB ID : 3d83

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-05-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.220	8.290	8.290	0.070	8.360	2

List of CHEMBLId :

CHEMBL476351

Binding Site :

Uniprot Annotation

Name:	Mitogen-activated protein kinase 14
ID:	MK14_HUMAN
AC:	Q16539
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	34.716
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.108	688.500

% Hydrophobic	% Polar
45.10	54.90
According to VolSite

Ligand :

HET Code:	GK6
Formula:	C28H30N4O3
Molecular weight:	470.563 g/mol
DrugBank ID:	-
Buried Surface Area:	61.92 %
Polar Surface area:	83.56 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
42.1691	30.1702	34.5887

Binding mode :

What is Poseview ?

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C26	CB	VAL- 30	4.12	0	Hydrophobic	false
C19	CG2	VAL- 38	4.12	0	Hydrophobic	false
C20	CG1	VAL- 38	3.81	0	Hydrophobic	false
C1	CB	ALA- 51	3.76	0	Hydrophobic	false
C22	CB	ALA- 51	3.34	0	Hydrophobic	false
C1	CB	LYS- 53	3.76	0	Hydrophobic	false
N1	OE2	GLU- 71	2.85	155.32	H-Bond (Ligand Donor)	false
C8	CG	GLU- 71	4.02	0	Hydrophobic	false
C15	CD2	LEU- 74	3.93	0	Hydrophobic	false
C4	CD1	LEU- 75	3.51	0	Hydrophobic	false
C7	CD2	LEU- 75	3.93	0	Hydrophobic	false
C13	SD	MET- 78	4	0	Hydrophobic	false
C13	CG1	VAL- 83	3.8	0	Hydrophobic	false
C11	CG2	ILE- 84	4.1	0	Hydrophobic	false
C12	CG2	ILE- 84	4.17	0	Hydrophobic	false
C4	CD1	LEU- 104	3.96	0	Hydrophobic	false
C3	CB	LEU- 104	3.89	0	Hydrophobic	false
C23	CB	THR- 106	4.46	0	Hydrophobic	false
C2	CG2	THR- 106	3.84	0	Hydrophobic	false
C3	CG2	THR- 106	3.77	0	Hydrophobic	false
O3	N	MET- 109	3.09	147.03	H-Bond (Protein Donor)	false
C22	CG	MET- 109	3.73	0	Hydrophobic	false
C14	CG2	ILE- 141	4.25	0	Hydrophobic	false
C13	CD1	ILE- 141	3.77	0	Hydrophobic	false
C14	CG2	ILE- 146	3.87	0	Hydrophobic	false
C14	CB	HIS- 148	4.41	0	Hydrophobic	false
C13	CG2	ILE- 166	4.15	0	Hydrophobic	false
C16	CD1	LEU- 167	4.41	0	Hydrophobic	false
C23	CD1	LEU- 167	4.01	0	Hydrophobic	false
O1	N	ASP- 168	3.13	168.39	H-Bond (Protein Donor)	false
C7	CB	ASP- 168	3.7	0	Hydrophobic	false
C27	CE1	PHE- 169	3.83	0	Hydrophobic	false