scPDB - 1nzq entry

Protein Data Bank Entry:

PDB ID : 1nzq

Resolution :2.180 Å

Experimental Method : X-ray

Deposition Date : 2003-02-19

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:	21.753
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.802	479.250

% Hydrophobic	% Polar
46.48	53.52
According to VolSite

Ligand :

HET Code:	162
Formula:	C23H33N6O4
Molecular weight:	457.546 g/mol
DrugBank ID:	-
Buried Surface Area:	58.06 %
Polar Surface area:	164.38 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
16.3346	19.9216	22.8607

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
C17	CD2	LEU- 99	4.12	0	Hydrophobic	false
C16	CG1	ILE- 174	4.42	0	Hydrophobic	false
N	OD1	ASP- 189	2.92	160.12	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 189	3.26	147.33	H-Bond (Ligand Donor)	false
C	OD1	ASP- 189	3.91	0	Ionic (Ligand Cationic)	false
C	OD2	ASP- 189	3.86	0	Ionic (Ligand Cationic)	false
N3	O	SER- 214	2.74	177.93	H-Bond (Ligand Donor)	false
C16	CE3	TRP- 215	3.64	0	Hydrophobic	false
C17	CD2	TRP- 215	4.29	0	Hydrophobic	false
C15	CB	TRP- 215	4.27	0	Hydrophobic	false
O1	N	GLY- 216	2.98	165.41	H-Bond (Protein Donor)	false
N5	O	GLY- 216	2.76	173	H-Bond (Ligand Donor)	false
O3	N	GLY- 219	3.05	165.44	H-Bond (Protein Donor)	false
N	O	GLY- 219	2.97	126.15	H-Bond (Ligand Donor)	false
C2	SG	CYS- 220	3.87	0	Hydrophobic	false
O3	O	HOH- 287	3.18	179.98	H-Bond (Protein Donor)	false