scPDB - 1afe entry

Protein Data Bank Entry:

PDB ID : 1afe

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1997-03-06

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:	34.755
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.849	479.250

% Hydrophobic	% Polar
47.89	52.11
According to VolSite

Ligand :

HET Code:	ALZ
Formula:	C17H27N4O3
Molecular weight:	335.421 g/mol
DrugBank ID:	DB07366
Buried Surface Area:	52.18 %
Polar Surface area:	98.31 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
16.9153	-14.6578	22.9937

Binding mode :

What is Poseview ?

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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- 60	3.59	0	Hydrophobic	false
C11	CH2	TRP- 60	3.9	0	Hydrophobic	false
C10	CD1	LEU- 99	4.01	0	Hydrophobic	false
C20	CD1	ILE- 174	3.41	0	Hydrophobic	false
C21	CG1	ILE- 174	4.2	0	Hydrophobic	false
C22	CD1	ILE- 174	4.22	0	Hydrophobic	false
N1	OD1	ASP- 189	3.5	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 189	2.67	0	Ionic (Ligand Cationic)	false
N1	O	ALA- 190	2.88	152.19	H-Bond (Ligand Donor)	false
C3	CB	ALA- 190	4.21	0	Hydrophobic	false
N6	OG	SER- 195	2.88	147.71	H-Bond (Ligand Donor)	false
C5	CG1	VAL- 213	4.41	0	Hydrophobic	false
N7	O	SER- 214	3.08	147.89	H-Bond (Ligand Donor)	false
O14	N	GLY- 216	3.21	172.84	H-Bond (Protein Donor)	false
C21	CG	GLU- 217	3.59	0	Hydrophobic	false
N1	O	GLY- 219	2.67	150.03	H-Bond (Ligand Donor)	false