scPDB - 1a4w entry

Protein Data Bank Entry:

PDB ID : 1a4w

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1998-02-06

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:	23.934
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.266	496.125

% Hydrophobic	% Polar
36.05	63.95
According to VolSite

Ligand :

HET Code:	QWE
Formula:	C29H40N7O4S2
Molecular weight:	614.802 g/mol
DrugBank ID:	-
Buried Surface Area:	50.89 %
Polar Surface area:	199.94 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
16.9607	-14.6646	21.0782

Binding mode :

What is Poseview ?

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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
C51	CB	HIS- 57	4.48	0	Hydrophobic	false
C31	CH2	TRP- 60	3.43	0	Hydrophobic	false
C2'	CZ3	TRP- 60	4.28	0	Hydrophobic	false
S1	CZ3	TRP- 60	3.6	0	Hydrophobic	false
CM1	CE1	TYR- 60	4.44	0	Hydrophobic	false
C41	CD2	TYR- 60	4.08	0	Hydrophobic	false
C51	CE1	TYR- 60	4.35	0	Hydrophobic	false
CM1	CD1	LEU- 99	3.6	0	Hydrophobic	false
C51	CD2	LEU- 99	3.61	0	Hydrophobic	false
C6	CD1	ILE- 174	4.27	0	Hydrophobic	false
NH2	OD2	ASP- 189	3.18	153.59	H-Bond (Ligand Donor)	false
C6	CB	TRP- 215	4.42	0	Hydrophobic	false
O	N	GLY- 216	2.98	162.97	H-Bond (Protein Donor)	false
C7	CG	GLU- 217	4.08	0	Hydrophobic	false
O2S	N	GLY- 219	3.36	152.89	H-Bond (Protein Donor)	false
NE	O	GLY- 219	3.03	127.28	H-Bond (Ligand Donor)	false
CD	SG	CYS- 220	3.92	0	Hydrophobic	false
NH1	O	HOH- 409	3.15	155.15	H-Bond (Ligand Donor)	false