scPDB - 1riw entry

Protein Data Bank Entry:

PDB ID : 1riw

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2003-11-18

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	31 %
C	69 %

Ligand binding site composition:

B-Factor:	23.651
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.232	550.125

% Hydrophobic	% Polar
36.20	63.80
According to VolSite

Ligand :

HET Code:	OSC
Formula:	C34H45N6O5
Molecular weight:	617.758 g/mol
DrugBank ID:	-
Buried Surface Area:	52.52 %
Polar Surface area:	173.81 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
16.4958	-14.5788	22.4654

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	CZ	TYR- 83	3.37	0	Hydrophobic	false
C17	CE2	TYR- 83	3.62	0	Hydrophobic	false
C12	CZ2	TRP- 86	3.53	0	Hydrophobic	false
C28	CD2	LEU- 132	4.41	0	Hydrophobic	false
C34	CD1	LEU- 132	4.28	0	Hydrophobic	false
C7	CD2	LEU- 132	3.79	0	Hydrophobic	false
C42	CG	GLU- 182	4.39	0	Hydrophobic	false
C28	CG2	ILE- 209	4.13	0	Hydrophobic	false
C23	CG1	ILE- 209	4.21	0	Hydrophobic	false
C40	OD2	ASP- 229	3.62	0	Ionic (Ligand Cationic)	false
C40	OD1	ASP- 229	3.57	0	Ionic (Ligand Cationic)	false
N43	OD1	ASP- 229	2.73	154.31	H-Bond (Ligand Donor)	false
N44	OD2	ASP- 229	2.82	151.09	H-Bond (Ligand Donor)	false
C22	CB	SER- 235	3.93	0	Hydrophobic	false
C22	CG1	VAL- 255	3.99	0	Hydrophobic	false
C32	CG1	VAL- 255	3.95	0	Hydrophobic	false
N13	O	SER- 256	2.99	152.59	H-Bond (Ligand Donor)	false
C15	CE3	TRP- 257	4.32	0	Hydrophobic	false
C23	CB	TRP- 257	3.77	0	Hydrophobic	false
O10	N	GLY- 258	2.88	171.67	H-Bond (Protein Donor)	false
N16	O	GLY- 258	2.99	159.99	H-Bond (Ligand Donor)	false
O31	N	GLY- 260	3.1	164.87	H-Bond (Protein Donor)	false
N43	O	GLY- 260	2.79	155.43	H-Bond (Ligand Donor)	false
C37	SG	CYS- 261	4.15	0	Hydrophobic	false
N43	O	HOH- 1067	3.33	127.24	H-Bond (Ligand Donor)	false