scPDB - 3qwc entry

Protein Data Bank Entry:

PDB ID : 3qwc

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2011-02-28

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:	21.420
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.580	516.375

% Hydrophobic	% Polar
41.18	58.82
According to VolSite

Ligand :

HET Code:	98P
Formula:	C21H27ClN4O2
Molecular weight:	402.918 g/mol
DrugBank ID:	-
Buried Surface Area:	60.81 %
Polar Surface area:	80.93 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
16.8104	-12.5072	22.3832

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
C14	CB	HIS- 57	4.43	0	Hydrophobic	false
C15	CH2	TRP- 60	3.95	0	Hydrophobic	false
C15	CZ	TYR- 60	3.59	0	Hydrophobic	false
C7	CD1	LEU- 99	4.19	0	Hydrophobic	false
C8	CD2	LEU- 99	4.02	0	Hydrophobic	false
C14	CD2	LEU- 99	3.81	0	Hydrophobic	false
C9	CD1	ILE- 174	3.63	0	Hydrophobic	false
CL28	CB	ALA- 190	4.36	0	Hydrophobic	false
CL28	CG1	VAL- 213	3.21	0	Hydrophobic	false
N24	O	SER- 214	3.07	173.87	H-Bond (Ligand Donor)	false
C2	CE3	TRP- 215	4.19	0	Hydrophobic	false
C9	CB	TRP- 215	3.67	0	Hydrophobic	false
N22	O	GLY- 216	2.98	175.36	H-Bond (Ligand Donor)	false
O26	N	GLY- 216	2.96	168.81	H-Bond (Protein Donor)	false
C2	CG	GLU- 217	4.38	0	Hydrophobic	false