scPDB - 4dtk entry

Protein Data Bank Entry:

PDB ID : 4dtk

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2012-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase pim-1
ID:	PIM1_HUMAN
AC:	P11309
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:	41.474
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.772	671.625

% Hydrophobic	% Polar
51.76	48.24
According to VolSite

Ligand :

HET Code:	7LI
Formula:	C18H23N3O3S
Molecular weight:	361.459 g/mol
DrugBank ID:	-
Buried Surface Area:	67.42 %
Polar Surface area:	113.65 Å2

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

Mass center Coordinates

X	Y	Z
18.9795	-37.3136	-1.12312

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
C	CD1	LEU- 44	3.86	0	Hydrophobic	false
C3	CD1	LEU- 44	4.32	0	Hydrophobic	false
C9	CB	LEU- 44	3.74	0	Hydrophobic	false
C10	CZ	PHE- 49	3.95	0	Hydrophobic	false
C9	CG1	VAL- 52	3.94	0	Hydrophobic	false
C10	CB	VAL- 52	4.16	0	Hydrophobic	false
C7	CG1	VAL- 52	4.02	0	Hydrophobic	false
C6	CB	ALA- 65	3.47	0	Hydrophobic	false
O1	NZ	LYS- 67	3.41	120.57	H-Bond (Protein Donor)	false
N2	NZ	LYS- 67	2.91	172.64	H-Bond (Protein Donor)	false
S	CG1	ILE- 104	4.09	0	Hydrophobic	false
S	CD1	LEU- 120	3.85	0	Hydrophobic	false
C4	CG	ARG- 122	4.41	0	Hydrophobic	false
C5	CB	ARG- 122	4.39	0	Hydrophobic	false
C1	CG1	VAL- 126	3.54	0	Hydrophobic	false
N1	OD2	ASP- 128	2.93	147.13	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 128	2.93	0	Ionic (Ligand Cationic)	false
N1	O	GLU- 171	3.03	139.15	H-Bond (Ligand Donor)	false
C13	CD2	LEU- 174	4.14	0	Hydrophobic	false
C2	CD2	LEU- 174	3.93	0	Hydrophobic	false
C3	CD2	LEU- 174	3.88	0	Hydrophobic	false
C4	CD1	LEU- 174	3.58	0	Hydrophobic	false
S	CB	ILE- 185	3.79	0	Hydrophobic	false
C13	CD1	ILE- 185	3.79	0	Hydrophobic	false
C7	CD1	ILE- 185	4.3	0	Hydrophobic	false
O2	N	ASP- 186	2.93	157.44	H-Bond (Protein Donor)	false
O2	O	HOH- 510	2.71	179.97	H-Bond (Protein Donor)	false