scPDB - 1nfy entry

Protein Data Bank Entry:

PDB ID : 1nfy

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2002-12-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.890	8.930	8.890	0.050	9.000	3

List of CHEMBLId :

CHEMBL48813

Binding Site :

Uniprot Annotation

Name:	Coagulation factor X
ID:	FA10_HUMAN
AC:	P00742
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.21.6

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	22.639
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.092	317.250

% Hydrophobic	% Polar
27.66	72.34
According to VolSite

Ligand :

HET Code:	RTR
Formula:	C20H20ClN4O3S2
Molecular weight:	463.981 g/mol
DrugBank ID:	DB08495
Buried Surface Area:	62.16 %
Polar Surface area:	145.91 Å2

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

Mass center Coordinates

X	Y	Z
7.80553	5.56357	22.4036

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
CL	CB	ALA- 190	3.8	0	Hydrophobic	false
C15	CB	ALA- 190	3.6	0	Hydrophobic	false
O8	NE2	GLN- 192	3.28	125.62	H-Bond (Protein Donor)	false
C10	CG1	VAL- 213	3.5	0	Hydrophobic	false
C25	CE3	TRP- 215	3.39	0	Hydrophobic	false
O20	N	GLY- 218	2.92	152.78	H-Bond (Protein Donor)	false
C6	SG	CYS- 220	4.35	0	Hydrophobic	false
CL	CZ	TYR- 228	3.43	0	Hydrophobic	false
N29	O	HOH- 331	2.97	174.08	H-Bond (Ligand Donor)	false