scPDB - 1dm2 entry

Protein Data Bank Entry:

PDB ID : 1dm2

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1999-12-13

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:	34.188
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.605	536.625

% Hydrophobic	% Polar
45.91	54.09
According to VolSite

Ligand :

HET Code:	HMD
Formula:	C11H11BrN5O2
Molecular weight:	325.141 g/mol
DrugBank ID:	DB02950
Buried Surface Area:	65.5 %
Polar Surface area:	110.88 Å2

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

Mass center Coordinates

X	Y	Z
27.1442	29.2	27.0323

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
C7	CG1	VAL- 18	4.27	0	Hydrophobic	false
C7	CB	ALA- 31	3.91	0	Hydrophobic	false
C7	CD2	PHE- 80	3.83	0	Hydrophobic	false
N2	O	GLU- 81	2.76	164.97	H-Bond (Ligand Donor)	false
O1	N	LEU- 83	2.74	163.5	H-Bond (Protein Donor)	false
N1	O	LEU- 83	3.17	165.46	H-Bond (Ligand Donor)	false
BR1	CB	ASP- 86	4.4	0	Hydrophobic	false
BR1	CD2	LEU- 134	4.23	0	Hydrophobic	false
N3	OD2	ASP- 145	3.41	123.62	H-Bond (Ligand Donor)	false
N5	OD2	ASP- 145	3.02	149.16	H-Bond (Ligand Donor)	false