scPDB - 3rmf entry

Protein Data Bank Entry:

PDB ID : 3rmf

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2011-04-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclin-dependent kinase 2
ID:	CDK2_HUMAN
AC:	P24941
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	22.596
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.928	610.875

% Hydrophobic	% Polar
50.28	49.72
According to VolSite

Ligand :

HET Code:	20Z
Formula:	C20H16N4O3S2
Molecular weight:	424.496 g/mol
DrugBank ID:	-
Buried Surface Area:	63.43 %
Polar Surface area:	164.79 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
92.6745	80.0975	-47.8354

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
S28	CD1	ILE- 10	3.79	0	Hydrophobic	false
C08	CD1	ILE- 10	3.82	0	Hydrophobic	false
C12	CB	VAL- 18	3.79	0	Hydrophobic	false
S28	CG2	VAL- 18	4.47	0	Hydrophobic	false
C11	CG2	VAL- 18	3.7	0	Hydrophobic	false
C13	CG1	VAL- 18	4.07	0	Hydrophobic	false
S28	CB	ALA- 31	4.4	0	Hydrophobic	false
C12	CD	LYS- 33	4.18	0	Hydrophobic	false
N03	O	GLU- 81	2.79	139.57	H-Bond (Ligand Donor)	false
N01	N	LEU- 83	3.27	174.75	H-Bond (Protein Donor)	false
N04	OD2	ASP- 86	2.92	147.42	H-Bond (Ligand Donor)	false
C19	CB	ASP- 86	4	0	Hydrophobic	false
O26	N	ASP- 86	3.1	167.13	H-Bond (Protein Donor)	false
O27	NZ	LYS- 89	3.34	170.94	H-Bond (Protein Donor)	false
C24	CB	ASN- 132	4.11	0	Hydrophobic	false
C20	CD2	LEU- 134	4.12	0	Hydrophobic	false
S28	CD1	LEU- 134	3.9	0	Hydrophobic	false
C15	CB	ALA- 144	4.28	0	Hydrophobic	false
C13	CB	ASP- 145	3.72	0	Hydrophobic	false
O27	O	HOH- 333	3.46	179.98	H-Bond (Protein Donor)	false