scPDB - 1wvy entry

Protein Data Bank Entry:

PDB ID : 1wvy

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2004-12-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.850	8.850	8.850	0.000	8.850	2

List of CHEMBLId :

CHEMBL388978

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:	32.803
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.938	432.000

% Hydrophobic	% Polar
57.03	42.97
According to VolSite

Ligand :

HET Code:	STU
Formula:	C28H27N4O3
Molecular weight:	467.539 g/mol
DrugBank ID:	DB02010
Buried Surface Area:	58.99 %
Polar Surface area:	74.03 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	8
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
26.2429	40.0502	10.5685

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
C25	CB	LEU- 19	4.31	0	Hydrophobic	false
C20	CB	LEU- 19	3.84	0	Hydrophobic	false
C3	CD2	LEU- 19	3.63	0	Hydrophobic	false
C25	CG2	VAL- 27	4.18	0	Hydrophobic	false
C13	CG1	VAL- 27	4.36	0	Hydrophobic	false
C21	CG2	VAL- 27	4.05	0	Hydrophobic	false
C18	CG2	VAL- 27	3.69	0	Hydrophobic	false
C17	CG1	VAL- 27	3.63	0	Hydrophobic	false
C17	CG1	VAL- 27	3.63	0	Hydrophobic	false
C7	CB	ALA- 40	4.14	0	Hydrophobic	false
C14	CD	LYS- 42	3.49	0	Hydrophobic	false
C13	CD1	LEU- 93	3.62	0	Hydrophobic	false
N1	O	GLU- 94	2.91	165.03	H-Bond (Ligand Donor)	false
O5	N	VAL- 96	2.66	171.22	H-Bond (Protein Donor)	false
C27	CG	GLU- 143	3.88	0	Hydrophobic	false
N4	OE2	GLU- 143	2.75	164.3	H-Bond (Ligand Donor)	false
N4	OE2	GLU- 143	2.75	0	Ionic (Ligand Cationic)	false
C6	SD	MET- 146	4.27	0	Hydrophobic	false
C3	CE	MET- 146	3.89	0	Hydrophobic	false
C27	CD1	ILE- 160	3.75	0	Hydrophobic	false
C11	CD1	ILE- 160	4.19	0	Hydrophobic	false
C15	CB	ASP- 161	3.91	0	Hydrophobic	false
N4	O	HOH- 2005	2.72	159.2	H-Bond (Ligand Donor)	false