scPDB - 2gde entry

Protein Data Bank Entry:

PDB ID : 2gde

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-03-16

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:	44.703
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.722	833.625

% Hydrophobic	% Polar
43.32	56.68
According to VolSite

Ligand :

HET Code:	SN3
Formula:	C26H43ClN6O10S
Molecular weight:	667.172 g/mol
DrugBank ID:	-
Buried Surface Area:	52.25 %
Polar Surface area:	257.85 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
16.2231	-14.5611	22.3991

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
C1	CE2	TYR- 60	3.6	0	Hydrophobic	false
C2	CZ	TYR- 60	3.31	0	Hydrophobic	false
C6	CZ2	TRP- 60	3.44	0	Hydrophobic	false
C10	CD1	LEU- 99	4.2	0	Hydrophobic	false
C30	CG1	ILE- 174	3.65	0	Hydrophobic	false
C20	OD1	ASP- 189	3.34	0	Ionic (Ligand Cationic)	false
C20	OD2	ASP- 189	3.35	0	Ionic (Ligand Cationic)	false
N21	OD2	ASP- 189	3.34	120.24	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 189	2.56	144.31	H-Bond (Ligand Donor)	false
C16	CB	ALA- 190	4.46	0	Hydrophobic	false
C14	CB	SER- 195	3.94	0	Hydrophobic	false
C14	CG1	VAL- 213	3.94	0	Hydrophobic	false
C16	CG1	VAL- 213	3.86	0	Hydrophobic	false
N12	O	SER- 214	3.04	170.55	H-Bond (Ligand Donor)	false
C30	CE3	TRP- 215	4.13	0	Hydrophobic	false
CL31	CE3	TRP- 215	3.91	0	Hydrophobic	false
O25	N	GLY- 216	2.95	164.69	H-Bond (Protein Donor)	false
N32	O	GLY- 216	2.88	159.78	H-Bond (Ligand Donor)	false
C30	CG	GLU- 217	3.92	0	Hydrophobic	false
N21	O	GLY- 219	2.72	158.54	H-Bond (Ligand Donor)	false
O35	N	GLY- 219	2.71	133.45	H-Bond (Protein Donor)	false
O38	N	GLY- 219	3.03	133.23	H-Bond (Protein Donor)	false
C18	SG	CYS- 220	4.11	0	Hydrophobic	false
C36	SG	CYS- 220	4.33	0	Hydrophobic	false
O41	NH1	ARG- 221	3.26	141.75	H-Bond (Protein Donor)	false
O41	NH2	ARG- 221	3.28	140.81	H-Bond (Protein Donor)	false
O41	CZ	ARG- 221	3.7	0	Ionic (Protein Cationic)	false