scPDB - 1c5n entry

Protein Data Bank Entry:

PDB ID : 1c5n

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 1999-12-22

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:	25.744
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.488	330.750

% Hydrophobic	% Polar
41.84	58.16
According to VolSite

Ligand :

HET Code:	ESI
Formula:	C9H8IN2S
Molecular weight:	303.143 g/mol
DrugBank ID:	DB03136
Buried Surface Area:	55.45 %
Polar Surface area:	79.84 Å2

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

Mass center Coordinates

X	Y	Z
12.5078	-12.6822	22.2344

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
C0	OD1	ASP- 189	3.72	0	Ionic (Ligand Cationic)	false
C0	OD2	ASP- 189	3.56	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 189	2.81	136.08	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 189	3.13	134.68	H-Bond (Ligand Donor)	false
S2	CB	ALA- 190	4.36	0	Hydrophobic	false
C6	CB	SER- 195	4.27	0	Hydrophobic	false
S2	CG1	VAL- 213	3.84	0	Hydrophobic	false
N1	O	GLY- 219	2.62	155.09	H-Bond (Ligand Donor)	false
I9	SG	CYS- 220	4.13	0	Hydrophobic	false