scPDB - 3r04 entry

Protein Data Bank Entry:

PDB ID : 3r04

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-03-07

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:	30.814
Number of residues:	34
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.351	529.875

% Hydrophobic	% Polar
60.51	39.49
According to VolSite

Ligand :

HET Code:	UNQ
Formula:	C19H20N4O3
Molecular weight:	352.387 g/mol
DrugBank ID:	-
Buried Surface Area:	54.3 %
Polar Surface area:	118.72 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
23.2409	-36.1421	1.11612

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
O12	O	HOH- 18	2.82	179.96	H-Bond (Protein Donor)	false
C01	CD1	LEU- 44	4.45	0	Hydrophobic	false
C20	CB	LEU- 44	4.1	0	Hydrophobic	false
C03	CG1	VAL- 52	3.99	0	Hydrophobic	false
C05	CB	ALA- 65	3.51	0	Hydrophobic	false
O11	NZ	LYS- 67	2.68	173.69	H-Bond (Protein Donor)	false
O11	NZ	LYS- 67	2.68	0	Ionic (Protein Cationic)	false
C06	CD1	ILE- 104	3.71	0	Hydrophobic	false
C06	CB	LEU- 120	4.22	0	Hydrophobic	false
N26	OD2	ASP- 128	3.14	0	Ionic (Ligand Cationic)	false
C24	CB	ASP- 128	4.06	0	Hydrophobic	false
C25	CD2	LEU- 174	3.94	0	Hydrophobic	false
C05	CD1	LEU- 174	3.66	0	Hydrophobic	false
C06	CG2	ILE- 185	4.35	0	Hydrophobic	false
C02	CD1	ILE- 185	4.05	0	Hydrophobic	false
O12	N	ASP- 186	2.96	154.63	H-Bond (Protein Donor)	false
N26	O	HOH- 327	3.01	142.98	H-Bond (Ligand Donor)	false
N26	O	HOH- 415	2.55	158.92	H-Bond (Ligand Donor)	false
N18	O	HOH- 504	3	173.22	H-Bond (Protein Donor)	false