scPDB - 3npc entry

Protein Data Bank Entry:

PDB ID : 3npc

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2010-06-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.140	8.220	8.200	0.080	8.340	4

List of CHEMBLId :

CHEMBL103667

Binding Site :

Uniprot Annotation

Name:	Mitogen-activated protein kinase 9
ID:	MK09_HUMAN
AC:	P45984
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.24

Chains:

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

Ligand binding site composition:

B-Factor:	20.548
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.589	945.000

% Hydrophobic	% Polar
41.43	58.57
According to VolSite

Ligand :

HET Code:	B96
Formula:	C31H38N5O3
Molecular weight:	528.665 g/mol
DrugBank ID:	DB03044
Buried Surface Area:	73.13 %
Polar Surface area:	81.85 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
54.4391	93.9756	24.0347

Binding mode :

What is Poseview ?

2D View
3D View

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
C6	CG2	VAL- 40	4.33	0	Hydrophobic	false
C34	CG1	VAL- 40	4.21	0	Hydrophobic	false
C42	CG1	VAL- 40	4.32	0	Hydrophobic	false
C34	CB	ALA- 53	3.79	0	Hydrophobic	false
C4	CD	LYS- 55	3.95	0	Hydrophobic	false
C34	CB	LYS- 55	4.1	0	Hydrophobic	false
C32	CB	LYS- 55	3.76	0	Hydrophobic	false
C25	CB	ARG- 69	3.52	0	Hydrophobic	false
N2	OE2	GLU- 73	2.75	145.34	H-Bond (Ligand Donor)	false
N9	OE2	GLU- 73	2.76	145.8	H-Bond (Ligand Donor)	false
C15	CG	GLU- 73	4.08	0	Hydrophobic	false
C22	CB	GLU- 73	3.68	0	Hydrophobic	false
C20	CD1	LEU- 76	3.84	0	Hydrophobic	false
C17	CD2	LEU- 77	4.24	0	Hydrophobic	false
C17	CG2	VAL- 80	4.49	0	Hydrophobic	false
C17	CG2	ILE- 85	4.43	0	Hydrophobic	false
C19	CG2	ILE- 85	4.18	0	Hydrophobic	false
C19	CG2	ILE- 86	4.27	0	Hydrophobic	false
C31	CD1	ILE- 86	3.5	0	Hydrophobic	false
C32	CD1	LEU- 88	4.18	0	Hydrophobic	false
C32	CB	LEU- 106	3.67	0	Hydrophobic	false
C32	CB	MET- 108	4.35	0	Hydrophobic	false
C46	SD	MET- 108	3.83	0	Hydrophobic	false
C5	SD	MET- 108	3.99	0	Hydrophobic	false
C34	CG	MET- 108	3.64	0	Hydrophobic	false
C48	CD1	LEU- 110	3.85	0	Hydrophobic	false
C46	CG	MET- 111	3.93	0	Hydrophobic	false
C48	CB	MET- 111	4.19	0	Hydrophobic	false
O47	N	MET- 111	2.8	170.29	H-Bond (Protein Donor)	false
C19	CD2	LEU- 142	4.38	0	Hydrophobic	false
C17	CD2	LEU- 142	3.97	0	Hydrophobic	false
C18	CG2	ILE- 147	4.08	0	Hydrophobic	false
C46	CG1	VAL- 158	4.39	0	Hydrophobic	false
C48	CG1	VAL- 158	4.48	0	Hydrophobic	false
C19	CG2	ILE- 167	4.49	0	Hydrophobic	false
C42	CD2	LEU- 168	4.37	0	Hydrophobic	false
C46	CD2	LEU- 168	4.3	0	Hydrophobic	false
C7	CD2	LEU- 168	3.92	0	Hydrophobic	false
O1	N	ASP- 169	2.98	172.6	H-Bond (Protein Donor)	false
C24	CB	ASP- 169	3.86	0	Hydrophobic	false
C7	CB	PHE- 170	4.29	0	Hydrophobic	false
C42	CZ	PHE- 170	3.52	0	Hydrophobic	false