scPDB - 2vd5 entry

Protein Data Bank Entry:

PDB ID : 2vd5

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Myotonin-protein kinase
ID:	DMPK_HUMAN
AC:	Q09013
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	58.975
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.276	543.375

% Hydrophobic	% Polar
52.17	47.83
According to VolSite

Ligand :

HET Code:	BI8
Formula:	C24H23N4O2
Molecular weight:	399.465 g/mol
DrugBank ID:	DB01946
Buried Surface Area:	56.98 %
Polar Surface area:	83.66 Å2

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

Mass center Coordinates

X	Y	Z
30.3217	-77.7811	14.7336

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
CB0	CD1	ILE- 77	4.26	0	Hydrophobic	false
CAR	CG1	ILE- 77	3.87	0	Hydrophobic	false
CAN	CD1	ILE- 77	3.33	0	Hydrophobic	false
CAQ	CB	VAL- 85	3.84	0	Hydrophobic	false
CAP	CG1	VAL- 85	3.68	0	Hydrophobic	false
CAB	CD	LYS- 100	3.69	0	Hydrophobic	false
CAC	CG	MET- 148	4.35	0	Hydrophobic	false
NAU	O	GLU- 149	2.95	145.47	H-Bond (Ligand Donor)	false
OAX	N	TYR- 151	2.89	170.09	H-Bond (Protein Donor)	false
NBC	OD1	ASN- 200	3.13	131.45	H-Bond (Ligand Donor)	false
CAY	CB	ALA- 212	4.26	0	Hydrophobic	false
CAE	CB	ALA- 212	4.3	0	Hydrophobic	false
NBC	OD2	ASP- 213	2.55	0	Ionic (Ligand Cationic)	false
CAY	CB	ASP- 213	3.96	0	Hydrophobic	false
CAF	CB	ASP- 213	3.61	0	Hydrophobic	false
OAZ	O	HOH- 2001	3.35	156.16	H-Bond (Protein Donor)	false