scPDB - 2zhw entry

Protein Data Bank Entry:

PDB ID : 2zhw

Resolution :2.020 Å

Experimental Method : X-ray

Deposition Date : 2008-02-08

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
H	100 %

Ligand binding site composition:

B-Factor:	35.093
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.914	435.375

% Hydrophobic	% Polar
46.51	53.49
According to VolSite

Ligand :

HET Code:	12U
Formula:	C22H35N5O2
Molecular weight:	401.546 g/mol
DrugBank ID:	DB06853
Buried Surface Area:	59.39 %
Polar Surface area:	117.63 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
15.6155	-12.0962	21.5118

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
C2	CZ3	TRP- 60	4.06	0	Hydrophobic	false
C3	CZ	TYR- 60	3.38	0	Hydrophobic	false
C3	CD1	LEU- 99	4.46	0	Hydrophobic	false
C9	OD2	ASP- 189	3.41	0	Ionic (Ligand Cationic)	false
C9	OD1	ASP- 189	3.46	0	Ionic (Ligand Cationic)	false
N10	OD2	ASP- 189	2.57	156.96	H-Bond (Ligand Donor)	false
N10	OD1	ASP- 189	3.46	123.03	H-Bond (Ligand Donor)	false
N11	OD2	ASP- 189	3.44	121.96	H-Bond (Ligand Donor)	false
N11	OD1	ASP- 189	2.66	151.5	H-Bond (Ligand Donor)	false
C27	CB	ALA- 190	4.12	0	Hydrophobic	false
C26	CG1	VAL- 213	3.95	0	Hydrophobic	false
N23	O	SER- 214	3.3	146.9	H-Bond (Ligand Donor)	false
N21	O	GLY- 216	2.74	148.89	H-Bond (Ligand Donor)	false
N10	O	GLY- 219	2.91	153.91	H-Bond (Ligand Donor)	false