scPDB - 1c4v entry

Protein Data Bank Entry:

PDB ID : 1c4v

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1999-09-25

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
2	100 %

Ligand binding site composition:

B-Factor:	21.575
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.528	394.875

% Hydrophobic	% Polar
43.59	56.41
According to VolSite

Ligand :

HET Code:	IH2
Formula:	C30H37N6O3
Molecular weight:	529.653 g/mol
DrugBank ID:	-
Buried Surface Area:	57.34 %
Polar Surface area:	124.57 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
16.9416	-14.4526	23.0815

Binding mode :

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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	3.74	0	Hydrophobic	false
C17	CZ	TYR- 60	4.18	0	Hydrophobic	false
C16	CE2	TYR- 60	3.87	0	Hydrophobic	false
C17	CZ2	TRP- 60	3.63	0	Hydrophobic	false
C16	CZ3	TRP- 60	3.75	0	Hydrophobic	false
C13	CD1	LEU- 99	4.1	0	Hydrophobic	false
C16	CD2	LEU- 99	4.49	0	Hydrophobic	false
C29	CD1	LEU- 99	3.69	0	Hydrophobic	false
C30	CD1	ILE- 174	3.38	0	Hydrophobic	false
C29	CG2	ILE- 174	3.87	0	Hydrophobic	false
C25	CD1	ILE- 174	3.59	0	Hydrophobic	false
C33	CD1	ILE- 174	3.34	0	Hydrophobic	false
N10	OD1	ASP- 189	2.56	159.02	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 189	3.28	126.09	H-Bond (Ligand Donor)	false
N11	OD2	ASP- 189	2.56	159.27	H-Bond (Ligand Donor)	false
C8	OD1	ASP- 189	3.44	0	Ionic (Ligand Cationic)	false
C8	OD2	ASP- 189	3.34	0	Ionic (Ligand Cationic)	false
C3	CB	ALA- 190	4.44	0	Hydrophobic	false
C3	CG1	VAL- 213	3.25	0	Hydrophobic	false
N9	O	SER- 214	3.12	157.91	H-Bond (Ligand Donor)	false
C13	CB	TRP- 215	3.71	0	Hydrophobic	false
C24	CE3	TRP- 215	4.21	0	Hydrophobic	false
C30	CB	TRP- 215	3.85	0	Hydrophobic	false
C30	CE3	TRP- 215	3.16	0	Hydrophobic	false
O22	N	GLY- 216	2.86	168.2	H-Bond (Protein Donor)	false
C33	CB	GLU- 217	3.57	0	Hydrophobic	false
N10	O	GLY- 219	2.82	150.71	H-Bond (Ligand Donor)	false