scPDB - 3c1k entry

Protein Data Bank Entry:

PDB ID : 3c1k

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 2008-01-23

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
A	100 %

Ligand binding site composition:

B-Factor:	29.410
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.770	604.125

% Hydrophobic	% Polar
40.22	59.78
According to VolSite

Ligand :

HET Code:	T15
Formula:	C26H34N6O5S
Molecular weight:	542.650 g/mol
DrugBank ID:	-
Buried Surface Area:	56.29 %
Polar Surface area:	150.87 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
16.0495	-14.7588	22.4739

Binding mode :

What is Poseview ?

2D View
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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
C16	CB	HIS- 57	4.41	0	Hydrophobic	false
C16	CH2	TRP- 60	4.06	0	Hydrophobic	false
C16	CZ	TYR- 60	3.54	0	Hydrophobic	false
C16	CD1	LEU- 99	3.78	0	Hydrophobic	false
C17	CD1	LEU- 99	3.99	0	Hydrophobic	false
C5	CG	LEU- 99	3.73	0	Hydrophobic	false
C33	CG	GLU- 146	3.42	0	Hydrophobic	false
C7	CD1	ILE- 174	3.87	0	Hydrophobic	false
C3	CD1	ILE- 174	3.91	0	Hydrophobic	false
C8	CB	ALA- 190	4.09	0	Hydrophobic	false
C33	SG	CYS- 191	3.95	0	Hydrophobic	false
C32	CB	GLU- 192	3.83	0	Hydrophobic	false
C8	CB	SER- 195	4.49	0	Hydrophobic	false
C8	CG1	VAL- 213	3.22	0	Hydrophobic	false
N20	O	SER- 214	3.22	154.81	H-Bond (Ligand Donor)	false
C4	CB	TRP- 215	4.38	0	Hydrophobic	false
C7	CE3	TRP- 215	4.1	0	Hydrophobic	false
C17	CB	TRP- 215	3.83	0	Hydrophobic	false
N9	O	GLY- 216	2.94	167.95	H-Bond (Ligand Donor)	false
O15	N	GLY- 216	3.06	164.4	H-Bond (Protein Donor)	false
C7	CG	GLU- 217	4.32	0	Hydrophobic	false
C33	SG	CYS- 220	3.36	0	Hydrophobic	false
N30	O	HOH- 914	2.92	173.77	H-Bond (Ligand Donor)	false