scPDB - 1c1w entry

Protein Data Bank Entry:

PDB ID : 1c1w

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1999-07-21

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:	24.461
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.268	705.375

% Hydrophobic	% Polar
38.28	61.72
According to VolSite

Ligand :

HET Code:	BAH
Formula:	C17H18N8O2
Molecular weight:	366.377 g/mol
DrugBank ID:	DB04301
Buried Surface Area:	55.36 %
Polar Surface area:	201.03 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	8
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
15.013	-12.8473	18.8064

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
C2'	SG	CYS- 42	4.37	0	Hydrophobic	false
DuAr	NZ	LYS- 60	3.71	47.37	Pi/Cation	false
C9	CH2	TRP- 60	4.22	0	Hydrophobic	false
C7	OD2	ASP- 195	3.59	0	Ionic (Ligand Cationic)	false
C7	OD1	ASP- 195	3.78	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 195	2.87	167.49	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 195	3.5	130.85	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 195	2.97	158.24	H-Bond (Ligand Donor)	false
C2	CB	ALA- 196	4.13	0	Hydrophobic	false
C9	CG	GLU- 198	4.33	0	Hydrophobic	false
C5'	CG	GLU- 198	3.94	0	Hydrophobic	false
N4'	OE2	GLU- 198	2.93	160.07	H-Bond (Ligand Donor)	false
C3	CB	SER- 201	4.29	0	Hydrophobic	false
C2	CG1	VAL- 219	3.6	0	Hydrophobic	false
N3'	ZN	ZN- 254	2.38	0	Metal Acceptor	false
N4	ZN	ZN- 255	2.56	0	Metal Acceptor	false