scPDB - 4bak entry

Protein Data Bank Entry:

PDB ID : 4bak

Resolution :1.940 Å

Experimental Method : X-ray

Deposition Date : 2012-09-14

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
B	100 %

Ligand binding site composition:

B-Factor:	21.761
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.865	418.500

% Hydrophobic	% Polar
48.39	51.61
According to VolSite

Ligand :

HET Code:	M67
Formula:	C25H40N6O3
Molecular weight:	472.623 g/mol
DrugBank ID:	-
Buried Surface Area:	65.23 %
Polar Surface area:	146.72 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
15.9429	-13.193	22.1659

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
C21	CB	HIS- 79	4.48	0	Hydrophobic	false
C21	CE2	TYR- 83	3.86	0	Hydrophobic	false
C21	CH2	TRP- 86	3.7	0	Hydrophobic	false
C16	CD2	LEU- 132	4.28	0	Hydrophobic	false
C21	CD2	LEU- 132	3.99	0	Hydrophobic	false
C2	CG	GLU- 182	4.5	0	Hydrophobic	false
C13	CG1	ILE- 209	3.65	0	Hydrophobic	false
C14	CD1	ILE- 209	3.73	0	Hydrophobic	false
C34	OD2	ASP- 229	3.62	0	Ionic (Ligand Cationic)	false
C34	OD1	ASP- 229	3.62	0	Ionic (Ligand Cationic)	false
N35	OD2	ASP- 229	2.81	156.12	H-Bond (Ligand Donor)	false
N36	OD1	ASP- 229	2.8	142.91	H-Bond (Ligand Donor)	false
C32	CB	ALA- 230	4.05	0	Hydrophobic	false
C1	SG	CYS- 231	4.2	0	Hydrophobic	false
C1	CG	GLU- 232	3.59	0	Hydrophobic	false
C32	CG1	VAL- 255	3.83	0	Hydrophobic	false
N26	O	SER- 256	3.29	164.81	H-Bond (Ligand Donor)	false
C11	CE3	TRP- 257	3.97	0	Hydrophobic	false
C15	CD2	TRP- 257	3.9	0	Hydrophobic	false
C16	CB	TRP- 257	4.04	0	Hydrophobic	false
C13	CE3	TRP- 257	4.03	0	Hydrophobic	false
N8	O	GLY- 258	2.87	166.52	H-Bond (Ligand Donor)	false
O18	N	GLY- 258	3.34	163.51	H-Bond (Protein Donor)	false
C13	CG	GLU- 259	4.17	0	Hydrophobic	false
O6	N	GLY- 260	2.94	164.45	H-Bond (Protein Donor)	false
N35	O	GLY- 260	2.84	142.77	H-Bond (Ligand Donor)	false
C30	SG	CYS- 261	4.38	0	Hydrophobic	false
C2	SG	CYS- 261	3.59	0	Hydrophobic	false