scPDB - 2xby entry

Protein Data Bank Entry:

PDB ID : 2xby

Resolution :2.020 Å

Experimental Method : X-ray

Deposition Date : 2010-04-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	22.143
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.175	266.625

% Hydrophobic	% Polar
30.38	69.62
According to VolSite

Ligand :

HET Code:	63C
Formula:	C26H26ClFN5O4
Molecular weight:	526.967 g/mol
DrugBank ID:	-
Buried Surface Area:	60.04 %
Polar Surface area:	112.04 Å2

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

Mass center Coordinates

X	Y	Z
9.99109	63.6951	3.85048

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
F30	CZ	TYR- 99	3.53	0	Hydrophobic	false
C31	CB	ALA- 190	3.81	0	Hydrophobic	false
C35	CG1	VAL- 213	3.64	0	Hydrophobic	false
C11	CB	TRP- 215	4.09	0	Hydrophobic	false
C16	CB	TRP- 215	3.55	0	Hydrophobic	false
N14	O	GLY- 218	2.79	171.27	H-Bond (Ligand Donor)	false
C3	SG	CYS- 220	4.49	0	Hydrophobic	false
C33	SG	CYS- 220	4.38	0	Hydrophobic	false
CL	CZ	TYR- 228	3.48	0	Hydrophobic	false