scPDB - 4i41 entry

Protein Data Bank Entry:

PDB ID : 4i41

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2012-11-27

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:	43.254
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.121	462.375

% Hydrophobic	% Polar
64.23	35.77
According to VolSite

Ligand :

HET Code:	MIX
Formula:	C22H28N4O6
Molecular weight:	444.481 g/mol
DrugBank ID:	DB01204
Buried Surface Area:	61.33 %
Polar Surface area:	177.99 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-17.7695	-37.1411	2.56937

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
CAZ	CB	LEU- 44	4.45	0	Hydrophobic	false
CAQ	CD1	PHE- 49	4.3	0	Hydrophobic	false
CBF	CG1	VAL- 52	4.19	0	Hydrophobic	false
CBE	CG2	VAL- 52	3.88	0	Hydrophobic	false
CBD	CG1	VAL- 52	4.06	0	Hydrophobic	false
CAH	CB	ALA- 65	3.36	0	Hydrophobic	false
CAG	CG2	ILE- 104	3.71	0	Hydrophobic	false
CAH	CD1	ILE- 104	4.21	0	Hydrophobic	false
CAG	CD1	LEU- 120	3.72	0	Hydrophobic	false
CAL	CG	GLN- 127	3.9	0	Hydrophobic	false
NAT	OD2	ASP- 128	3.42	147.56	H-Bond (Ligand Donor)	false
NAT	OD2	ASP- 128	3.42	0	Ionic (Ligand Cationic)	false
OAD	N	ASP- 128	2.87	172.55	H-Bond (Protein Donor)	false
OAD	OD2	ASP- 131	2.57	173.52	H-Bond (Ligand Donor)	false
OAC	OD2	ASP- 167	3.1	170.05	H-Bond (Ligand Donor)	false
NAS	OE1	GLU- 171	3.92	0	Ionic (Ligand Cationic)	false
NAS	OD1	ASN- 172	2.83	145.08	H-Bond (Ligand Donor)	false
CAR	CD2	LEU- 174	4.17	0	Hydrophobic	false
CAX	CD1	LEU- 174	3.54	0	Hydrophobic	false
CAQ	CD1	ILE- 185	3.9	0	Hydrophobic	false
CBE	CD1	ILE- 185	3.76	0	Hydrophobic	false
CAW	CG2	ILE- 185	3.66	0	Hydrophobic	false
NAS	OD2	ASP- 186	3.05	166.56	H-Bond (Ligand Donor)	false
NAS	OD2	ASP- 186	3.05	0	Ionic (Ligand Cationic)	false
CAQ	CB	ASP- 186	3.74	0	Hydrophobic	false