scPDB - 2bxt entry

Protein Data Bank Entry:

PDB ID : 2bxt

Resolution :1.830 Å

Experimental Method : X-ray

Deposition Date : 2005-07-27

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:	25.540
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.358	408.375

% Hydrophobic	% Polar
38.84	61.16
According to VolSite

Ligand :

HET Code:	C2D
Formula:	C22H34Cl2N5OS
Molecular weight:	487.509 g/mol
DrugBank ID:	DB07521
Buried Surface Area:	70.92 %
Polar Surface area:	110.93 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	3
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
11.9945	-13.1136	12.7617

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
CL3	CB	HIS- 57	4.01	0	Hydrophobic	false
CL3	CH2	TRP- 60	3.91	0	Hydrophobic	false
CL3	CE2	TYR- 60	3.58	0	Hydrophobic	false
CL3	CD1	LEU- 99	3.94	0	Hydrophobic	false
C16	CD1	LEU- 99	4.13	0	Hydrophobic	false
C30	CG	LEU- 99	4	0	Hydrophobic	false
C25	CD1	ILE- 174	3.9	0	Hydrophobic	false
C26	CD1	ILE- 174	3.83	0	Hydrophobic	false
C4	CB	ALA- 190	3.95	0	Hydrophobic	false
C6	CB	ALA- 190	3.9	0	Hydrophobic	false
N14	OE2	GLU- 192	2.75	132.21	H-Bond (Ligand Donor)	false
N14	OE2	GLU- 192	2.75	0	Ionic (Ligand Cationic)	false
N14	OG	SER- 195	2.91	144.67	H-Bond (Ligand Donor)	false
CL2	CG1	VAL- 213	3.63	0	Hydrophobic	false
C16	CB	TRP- 215	4.26	0	Hydrophobic	false
C25	CE3	TRP- 215	4.01	0	Hydrophobic	false
O1	N	GLY- 216	3.08	161.22	H-Bond (Protein Donor)	false
N23	O	GLY- 216	2.92	156.03	H-Bond (Ligand Donor)	false
C25	CG	GLU- 217	3.59	0	Hydrophobic	false
S10	SG	CYS- 220	3.42	0	Hydrophobic	false
C7	SG	CYS- 220	4.08	0	Hydrophobic	false
CL2	CZ	TYR- 228	4.07	0	Hydrophobic	false