scPDB - 3hat entry

Protein Data Bank Entry:

PDB ID : 3hat

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1994-10-16

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:	23.062
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.655	556.875

% Hydrophobic	% Polar
39.39	60.61
According to VolSite

Ligand :

HET Code:	GLY_VAL_ARG_RNG
Formula:	C19H36N8O5
Molecular weight:	456.540 g/mol
DrugBank ID:	-
Buried Surface Area:	58.76 %
Polar Surface area:	217.49 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	8
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
16.439	-13.7306	22.5454

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
CG2	CE2	TYR- 60	4.04	0	Hydrophobic	false
CG1	CZ	TYR- 60	3.39	0	Hydrophobic	false
CG1	CZ2	TRP- 60	4.17	0	Hydrophobic	false
CG2	CH2	TRP- 60	3.43	0	Hydrophobic	false
CB	CD1	LEU- 99	3.63	0	Hydrophobic	false
CH	CG1	ILE- 174	4.29	0	Hydrophobic	false
CG	CG2	ILE- 174	4.26	0	Hydrophobic	false
CF	CD1	ILE- 174	3.24	0	Hydrophobic	false
CZ	OD2	ASP- 189	3.51	0	Ionic (Ligand Cationic)	false
CZ	OD1	ASP- 189	3.88	0	Ionic (Ligand Cationic)	false
NH1	OD1	ASP- 189	3.19	145.57	H-Bond (Ligand Donor)	false
NH2	OD2	ASP- 189	2.51	136.48	H-Bond (Ligand Donor)	false
CD	CB	ALA- 190	4.38	0	Hydrophobic	false
O	N	SER- 195	2.78	134.77	H-Bond (Protein Donor)	false
OXT	OG	SER- 195	2.51	122.62	H-Bond (Protein Donor)	false
CB	CB	SER- 195	3.96	0	Hydrophobic	false
CB	CG1	VAL- 213	4.31	0	Hydrophobic	false
CD	CG1	VAL- 213	4.28	0	Hydrophobic	false
N	O	SER- 214	3.11	155.88	H-Bond (Ligand Donor)	false
CG	CZ3	TRP- 215	4.21	0	Hydrophobic	false
CH	CE3	TRP- 215	3.4	0	Hydrophobic	false
O	N	GLY- 216	3.18	147.45	H-Bond (Protein Donor)	false
CA	CG	GLU- 217	3.86	0	Hydrophobic	false
NH2	O	GLY- 219	3.15	170.73	H-Bond (Ligand Donor)	false