scPDB - 1yhs entry

Protein Data Bank Entry:

PDB ID : 1yhs

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2005-01-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.820	8.420	8.500	0.370	8.850	4

List of CHEMBLId :

CHEMBL388978

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:	29.945
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.294	614.250

% Hydrophobic	% Polar
60.99	39.01
According to VolSite

Ligand :

HET Code:	STU
Formula:	C28H27N4O3
Molecular weight:	467.539 g/mol
DrugBank ID:	DB02010
Buried Surface Area:	67.45 %
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
-18.8534	37.3442	-1.82277

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
C25	CB	LEU- 44	4.23	0	Hydrophobic	false
C6	CD1	LEU- 44	3.71	0	Hydrophobic	false
C1	CD2	LEU- 44	4.1	0	Hydrophobic	false
C5	CD1	LEU- 44	3.67	0	Hydrophobic	false
C22	CZ	PHE- 49	4.41	0	Hydrophobic	false
C26	CE2	PHE- 49	3.4	0	Hydrophobic	false
C27	CE1	PHE- 49	4.07	0	Hydrophobic	false
C15	CB	PHE- 49	3.71	0	Hydrophobic	false
C26	CB	VAL- 52	3.97	0	Hydrophobic	false
C11	CG1	VAL- 52	3.97	0	Hydrophobic	false
C17	CG2	VAL- 52	3.78	0	Hydrophobic	false
C10	CB	ALA- 65	3.91	0	Hydrophobic	false
C14	CD	LYS- 67	3.45	0	Hydrophobic	false
C13	CD2	LEU- 120	3.87	0	Hydrophobic	false
N1	O	GLU- 121	2.77	150.36	H-Bond (Ligand Donor)	false
C4	CD	ARG- 122	4.2	0	Hydrophobic	false
C2	CG1	VAL- 126	4.35	0	Hydrophobic	false
C3	CB	VAL- 126	3.63	0	Hydrophobic	false
C4	CG1	VAL- 126	4.1	0	Hydrophobic	false
C24	CB	ASP- 128	4.16	0	Hydrophobic	false
N4	OD1	ASP- 128	2.81	164.48	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 128	2.81	0	Ionic (Ligand Cationic)	false
N4	O	GLU- 171	2.9	149.99	H-Bond (Ligand Donor)	false
C24	CD1	LEU- 174	4.39	0	Hydrophobic	false
C19	CD1	LEU- 174	4.45	0	Hydrophobic	false
C4	CD2	LEU- 174	4.47	0	Hydrophobic	false
C6	CD2	LEU- 174	3.86	0	Hydrophobic	false
C7	CD2	LEU- 174	3.57	0	Hydrophobic	false
C24	CD1	ILE- 185	4.39	0	Hydrophobic	false
C22	CD1	ILE- 185	4.44	0	Hydrophobic	false
C10	CG2	ILE- 185	4.14	0	Hydrophobic	false
C13	CB	ILE- 185	4.13	0	Hydrophobic	false
C27	CD1	ILE- 185	3.89	0	Hydrophobic	false
C18	CD1	ILE- 185	3.89	0	Hydrophobic	false
C12	CD1	ILE- 185	3.89	0	Hydrophobic	false
C15	CB	ASP- 186	3.58	0	Hydrophobic	false