scPDB - 1wvx entry

Protein Data Bank Entry:

PDB ID : 1wvx

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2004-12-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Death-associated protein kinase 1
ID:	DAPK1_HUMAN
AC:	P53355
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	41.033
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.086	577.125

% Hydrophobic	% Polar
57.89	42.11
According to VolSite

Ligand :

HET Code:	BD4
Formula:	C19H20N3O2
Molecular weight:	322.381 g/mol
DrugBank ID:	DB07444
Buried Surface Area:	62.81 %
Polar Surface area:	78.74 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
28.2227	39.9636	9.7255

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
C14	CD2	LEU- 19	4.17	0	Hydrophobic	false
C3	CB	LEU- 19	3.51	0	Hydrophobic	false
C6	CD1	LEU- 19	3.57	0	Hydrophobic	false
C16	CG2	VAL- 27	3.9	0	Hydrophobic	false
C11	CG1	VAL- 27	4.08	0	Hydrophobic	false
C8	CG2	VAL- 27	3.79	0	Hydrophobic	false
C13	CB	ALA- 40	4.29	0	Hydrophobic	false
C15	CD1	LEU- 93	4.29	0	Hydrophobic	false
N21	O	GLU- 94	2.88	166.24	H-Bond (Ligand Donor)	false
C6	CD1	LEU- 95	4.36	0	Hydrophobic	false
C14	CD1	LEU- 95	4.35	0	Hydrophobic	false
O24	N	VAL- 96	2.99	168.82	H-Bond (Protein Donor)	false
C6	CG2	VAL- 96	4.03	0	Hydrophobic	false
N19	OE2	GLU- 100	2.86	142.25	H-Bond (Ligand Donor)	false
N19	OE2	GLU- 100	2.86	0	Ionic (Ligand Cationic)	false
N19	O	GLU- 143	2.86	146.64	H-Bond (Ligand Donor)	false
C17	CE	MET- 146	4.41	0	Hydrophobic	false
C5	CE	MET- 146	3.46	0	Hydrophobic	false
C10	CD1	ILE- 160	3.92	0	Hydrophobic	false