scPDB - 2zdu entry

Protein Data Bank Entry:

PDB ID : 2zdu

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-11-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mitogen-activated protein kinase 10
ID:	MK10_HUMAN
AC:	P53779
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.24

Chains:

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

Ligand binding site composition:

B-Factor:	30.675
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.281	438.750

% Hydrophobic	% Polar
59.23	40.77
According to VolSite

Ligand :

HET Code:	446
Formula:	C28H22BrN2O6
Molecular weight:	562.388 g/mol
DrugBank ID:	-
Buried Surface Area:	55.18 %
Polar Surface area:	115.84 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
17.1649	-11.8609	85.9503

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
C50	CB	LYS- 68	4.06	0	Hydrophobic	false
C3	CD1	ILE- 70	4.33	0	Hydrophobic	false
C32	CG1	ILE- 70	4.17	0	Hydrophobic	false
C39	CG2	ILE- 70	4.18	0	Hydrophobic	false
C41	CG2	ILE- 70	3.96	0	Hydrophobic	false
C42	CB	ILE- 70	4.32	0	Hydrophobic	false
C49	CG2	ILE- 70	4.1	0	Hydrophobic	false
C25	CD1	ILE- 70	4.33	0	Hydrophobic	false
C2	CG1	VAL- 78	3.95	0	Hydrophobic	false
C32	CB	VAL- 78	3.93	0	Hydrophobic	false
C6	CB	ALA- 91	3.48	0	Hydrophobic	false
BR14	CB	LYS- 93	4.45	0	Hydrophobic	false
C5	CD1	ILE- 124	4.44	0	Hydrophobic	false
C6	CG1	ILE- 124	4.32	0	Hydrophobic	false
BR14	SD	MET- 146	3.82	0	Hydrophobic	false
C6	CB	MET- 146	3.8	0	Hydrophobic	false
C5	CD1	LEU- 148	4.47	0	Hydrophobic	false
C38	CD1	LEU- 148	3.62	0	Hydrophobic	false
O24	N	MET- 149	2.7	153.3	H-Bond (Protein Donor)	false
C19	CB	ASN- 152	4.1	0	Hydrophobic	false
O23	ND2	ASN- 152	3.16	142.72	H-Bond (Protein Donor)	false
C5	CG2	VAL- 196	4.43	0	Hydrophobic	false
C16	CG1	VAL- 196	4.32	0	Hydrophobic	false
C4	CG1	VAL- 196	3.85	0	Hydrophobic	false
C28	CG1	VAL- 196	3.97	0	Hydrophobic	false
BR14	CD2	LEU- 206	4.18	0	Hydrophobic	false
C2	CD1	LEU- 206	3.66	0	Hydrophobic	false
C28	CD1	LEU- 206	3.58	0	Hydrophobic	false
C6	CD2	LEU- 206	3.61	0	Hydrophobic	false