scPDB - 2zdt entry

Protein Data Bank Entry:

PDB ID : 2zdt

Resolution :2.000 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:	28.815
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.069	533.250

% Hydrophobic	% Polar
52.53	47.47
According to VolSite

Ligand :

HET Code:	46C
Formula:	C26H19ClNO4
Molecular weight:	444.886 g/mol
DrugBank ID:	-
Buried Surface Area:	61.04 %
Polar Surface area:	77.51 Å2

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

Mass center Coordinates

X	Y	Z
47.705	7.32641	31.5471

Binding mode :

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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
O50	NZ	LYS- 68	3.65	0	Ionic (Protein Cationic)	false
O51	NZ	LYS- 68	2.78	0	Ionic (Protein Cationic)	false
O51	NZ	LYS- 68	2.78	175.59	H-Bond (Protein Donor)	false
C19	CG1	ILE- 70	4.26	0	Hydrophobic	false
C33	CB	ILE- 70	4.34	0	Hydrophobic	false
C39	CG1	ILE- 70	4.28	0	Hydrophobic	false
C3	CD1	ILE- 70	4.09	0	Hydrophobic	false
C30	CD1	ILE- 70	3.75	0	Hydrophobic	false
C31	CG2	ILE- 70	3.77	0	Hydrophobic	false
C1	CG1	VAL- 78	4.07	0	Hydrophobic	false
C2	CG1	VAL- 78	3.83	0	Hydrophobic	false
C40	CG2	VAL- 78	3.6	0	Hydrophobic	false
C6	CB	ALA- 91	3.38	0	Hydrophobic	false
CL14	CD	LYS- 93	4.26	0	Hydrophobic	false
C6	CD1	ILE- 124	4.21	0	Hydrophobic	false
C6	CB	MET- 146	3.99	0	Hydrophobic	false
CL14	CE	MET- 146	3.64	0	Hydrophobic	false
C5	CD1	LEU- 148	4.24	0	Hydrophobic	false
C30	CD1	LEU- 148	3.7	0	Hydrophobic	false
O16	N	MET- 149	2.85	149	H-Bond (Protein Donor)	false
C20	CB	ASN- 152	4.26	0	Hydrophobic	false
O18	ND2	ASN- 152	3.25	147.53	H-Bond (Protein Donor)	false
C26	CG1	VAL- 196	3.73	0	Hydrophobic	false
C4	CG1	VAL- 196	3.96	0	Hydrophobic	false
CL14	CD2	LEU- 206	4.39	0	Hydrophobic	false
C2	CD1	LEU- 206	3.74	0	Hydrophobic	false
C43	CD1	LEU- 206	3.48	0	Hydrophobic	false
C6	CD2	LEU- 206	3.79	0	Hydrophobic	false