scPDB - 2pks entry

Protein Data Bank Entry:

PDB ID : 2pks

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-04-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prothrombin
ID:	THRB_HUMAN
AC:	P00734
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.21.5

Chains:

Chain Name:	Percentage of Residues within binding site
B	22 %
C	78 %

Ligand binding site composition:

B-Factor:	33.488
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.787	432.000

% Hydrophobic	% Polar
46.88	53.13
According to VolSite

Ligand :

HET Code:	G44
Formula:	C21H21N4O
Molecular weight:	345.418 g/mol
DrugBank ID:	DB07809
Buried Surface Area:	54.93 %
Polar Surface area:	93.6 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
16.3218	-12.8463	22.8063

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
C11	CD1	LEU- 132	4.32	0	Hydrophobic	false
C3	CD1	ILE- 209	3.27	0	Hydrophobic	false
C23	OD1	ASP- 229	3.28	0	Ionic (Ligand Cationic)	false
C23	OD2	ASP- 229	3.38	0	Ionic (Ligand Cationic)	false
N24	OD1	ASP- 229	2.66	129.97	H-Bond (Ligand Donor)	false
C21	CB	ALA- 230	3.92	0	Hydrophobic	false
C21	CG1	VAL- 255	4.27	0	Hydrophobic	false
C5	CB	TRP- 257	3.78	0	Hydrophobic	false
C26	CB	TRP- 257	3.88	0	Hydrophobic	false
N24	O	GLY- 260	2.85	123.17	H-Bond (Ligand Donor)	false
C19	SG	CYS- 261	4.23	0	Hydrophobic	false