scPDB - 4bam entry

Protein Data Bank Entry:

PDB ID : 4bam

Resolution :1.880 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:	20.387
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.855	425.250

% Hydrophobic	% Polar
49.21	50.79
According to VolSite

Ligand :

HET Code:	MM9
Formula:	C24H38N6O3
Molecular weight:	458.597 g/mol
DrugBank ID:	-
Buried Surface Area:	63.38 %
Polar Surface area:	137.93 Å2

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

Mass center Coordinates

X	Y	Z
16.0222	-13.0126	22.1439

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
C26	CB	HIS- 79	4.32	0	Hydrophobic	false
C26	CE2	TYR- 83	3.92	0	Hydrophobic	false
C26	CH2	TRP- 86	3.73	0	Hydrophobic	false
C6	CD2	LEU- 132	4.48	0	Hydrophobic	false
C26	CD2	LEU- 132	3.89	0	Hydrophobic	false
C3	CG1	ILE- 209	3.69	0	Hydrophobic	false
C4	CD1	ILE- 209	3.72	0	Hydrophobic	false
C23	OD2	ASP- 229	3.66	0	Ionic (Ligand Cationic)	false
C23	OD1	ASP- 229	3.6	0	Ionic (Ligand Cationic)	false
N24	OD1	ASP- 229	2.81	144.63	H-Bond (Ligand Donor)	false
N25	OD2	ASP- 229	2.8	153.41	H-Bond (Ligand Donor)	false
C19	CB	ALA- 230	4	0	Hydrophobic	false
C19	CG1	VAL- 255	3.77	0	Hydrophobic	false
N15	O	SER- 256	3.21	166.67	H-Bond (Ligand Donor)	false
C1	CE3	TRP- 257	4.1	0	Hydrophobic	false
C6	CB	TRP- 257	4.1	0	Hydrophobic	false
C5	CE3	TRP- 257	3.92	0	Hydrophobic	false
N7	O	GLY- 258	2.92	152.03	H-Bond (Ligand Donor)	false
O0	N	GLY- 258	3.26	160	H-Bond (Protein Donor)	false
C3	CG	GLU- 259	4	0	Hydrophobic	false
N25	O	GLY- 260	2.83	147.62	H-Bond (Ligand Donor)	false
O30	N	GLY- 260	2.89	156.63	H-Bond (Protein Donor)	false
C21	SG	CYS- 261	4.35	0	Hydrophobic	false