scPDB - 2a2x entry

Protein Data Bank Entry:

PDB ID : 2a2x

Resolution :2.440 Å

Experimental Method : X-ray

Deposition Date : 2005-06-23

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:	27.188
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.565	523.125

% Hydrophobic	% Polar
45.81	54.19
According to VolSite

Ligand :

HET Code:	NA9
Formula:	C22H35N6O4
Molecular weight:	447.551 g/mol
DrugBank ID:	-
Buried Surface Area:	57.08 %
Polar Surface area:	170.64 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
16.5031	19.8691	22.8219

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
C15	CB	HIS- 57	4.32	0	Hydrophobic	false
C15	CH2	TRP- 60	4.37	0	Hydrophobic	false
C15	CD2	LEU- 99	3.77	0	Hydrophobic	false
C30	CD2	LEU- 99	4.38	0	Hydrophobic	false
C31	CB	LEU- 99	4.39	0	Hydrophobic	false
C32	CD2	LEU- 99	4.32	0	Hydrophobic	false
C31	CG2	ILE- 174	4.2	0	Hydrophobic	false
C8	OD2	ASP- 189	3.72	0	Ionic (Ligand Cationic)	false
C8	OD1	ASP- 189	3.55	0	Ionic (Ligand Cationic)	false
N9	OD1	ASP- 189	2.7	149.71	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 189	3.01	140.04	H-Bond (Ligand Donor)	false
N11	O	SER- 214	3.15	167.38	H-Bond (Ligand Donor)	false
C31	CD2	TRP- 215	4.36	0	Hydrophobic	false
C32	CE3	TRP- 215	3.55	0	Hydrophobic	false
O20	N	GLY- 216	3.15	167.38	H-Bond (Protein Donor)	false
N21	O	GLY- 216	3.07	170.36	H-Bond (Ligand Donor)	false
N9	O	GLY- 219	2.89	153.85	H-Bond (Ligand Donor)	false
O24	N	GLY- 219	2.79	156.24	H-Bond (Protein Donor)	false
C1	SG	CYS- 220	4.28	0	Hydrophobic	false