scPDB - 3dhk entry

Protein Data Bank Entry:

PDB ID : 3dhk

Resolution :1.730 Å

Experimental Method : X-ray

Deposition Date : 2008-06-18

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:	17.787
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.386	516.375

% Hydrophobic	% Polar
42.48	57.52
According to VolSite

Ligand :

HET Code:	23U
Formula:	C27H29ClN3O2
Molecular weight:	462.991 g/mol
DrugBank ID:	-
Buried Surface Area:	62.1 %
Polar Surface area:	77.05 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.8899	-13.2227	23.3711

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
C12	CZ	TYR- 60	3.62	0	Hydrophobic	false
C12	CH2	TRP- 60	3.82	0	Hydrophobic	false
C4	CD1	LEU- 99	3.93	0	Hydrophobic	false
C3	CD2	LEU- 99	3.98	0	Hydrophobic	false
C12	CD2	LEU- 99	4.12	0	Hydrophobic	false
C2	CD1	ILE- 174	4.3	0	Hydrophobic	false
C24	CD1	ILE- 174	3.93	0	Hydrophobic	false
CL1	CB	ALA- 190	3.89	0	Hydrophobic	false
C21	CB	ALA- 190	3.88	0	Hydrophobic	false
C22	CG1	VAL- 213	3.61	0	Hydrophobic	false
N23	O	SER- 214	2.88	176.28	H-Bond (Ligand Donor)	false
C8	CE3	TRP- 215	4.32	0	Hydrophobic	false
C2	CB	TRP- 215	3.65	0	Hydrophobic	false
N2	O	GLY- 216	2.88	169.66	H-Bond (Ligand Donor)	false
O32	N	GLY- 216	2.94	157.76	H-Bond (Protein Donor)	false
C23	CB	GLU- 217	3.94	0	Hydrophobic	false
C24	CG	GLU- 217	3.44	0	Hydrophobic	false
C19	SG	CYS- 220	4.23	0	Hydrophobic	false
CL1	CZ	TYR- 228	4.15	0	Hydrophobic	false