scPDB - 1ypk entry

Protein Data Bank Entry:

PDB ID : 1ypk

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2005-01-31

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:	21.165
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.806	509.625

% Hydrophobic	% Polar
45.70	54.30
According to VolSite

Ligand :

HET Code:	CCR
Formula:	C29H39N5O7S
Molecular weight:	601.714 g/mol
DrugBank ID:	DB03081
Buried Surface Area:	60.35 %
Polar Surface area:	204.92 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
17.1171	-13.4764	22.0422

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
C10	CZ2	TRP- 60	4.03	0	Hydrophobic	false
C62	CZ3	TRP- 60	3.44	0	Hydrophobic	false
C10	CZ	TYR- 60	4.45	0	Hydrophobic	false
C19	CE1	TYR- 60	3.99	0	Hydrophobic	false
C62	CD2	TYR- 60	3.76	0	Hydrophobic	false
C63	CZ	TYR- 60	3.55	0	Hydrophobic	false
C14	CG	LEU- 99	4.1	0	Hydrophobic	false
C19	CG	LEU- 99	3.9	0	Hydrophobic	false
C64	CD1	LEU- 99	3.84	0	Hydrophobic	false
C18	CD1	LEU- 99	4.01	0	Hydrophobic	false
C17	CD1	ILE- 174	4.44	0	Hydrophobic	false
C18	CD1	ILE- 174	3.93	0	Hydrophobic	false
C57	OD2	ASP- 189	3.66	0	Ionic (Ligand Cationic)	false
C57	OD1	ASP- 189	3.67	0	Ionic (Ligand Cationic)	false
N59	OD1	ASP- 189	2.93	140.89	H-Bond (Ligand Donor)	false
N58	OD2	ASP- 189	2.76	160.14	H-Bond (Ligand Donor)	false
C44	CB	SER- 195	4.16	0	Hydrophobic	false
C55	CG1	VAL- 213	3.99	0	Hydrophobic	false
C17	CE3	TRP- 215	3.4	0	Hydrophobic	false
C18	CD2	TRP- 215	3.76	0	Hydrophobic	false
O36	N	GLY- 216	3.06	161.21	H-Bond (Protein Donor)	false
C17	CG	GLU- 217	4.39	0	Hydrophobic	false
O34	N	GLY- 219	2.86	167.2	H-Bond (Protein Donor)	false
N58	O	GLY- 219	2.91	137.92	H-Bond (Ligand Donor)	false
C53	SG	CYS- 220	4.04	0	Hydrophobic	false
O43	O	HOH- 9191	3.26	147.29	H-Bond (Protein Donor)	false