scPDB - 5fsx entry

Protein Data Bank Entry:

PDB ID : 5fsx

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2016-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	C9ZP98_TRYB9
AC:	C9ZP98
Organism:	Trypanosoma brucei gambiense
Reign:	Eukaryota
TaxID:	679716
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.307
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	513.000

% Hydrophobic	% Polar
57.24	42.76
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	65.95 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
97.9008	32.0433	102.365

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
C5'	CB	ALA- 120	4.08	0	Hydrophobic	false
O2A	N	VAL- 131	2.94	166.88	H-Bond (Protein Donor)	false
C1'	CB	VAL- 131	4.05	0	Hydrophobic	false
C5'	CG1	VAL- 131	4.31	0	Hydrophobic	false
C4'	CB	CYS- 207	3.97	0	Hydrophobic	false
C3'	CB	CYS- 208	4.08	0	Hydrophobic	false
O3'	N	CYS- 208	3.1	144.37	H-Bond (Protein Donor)	false
O2B	N	SER- 210	2.79	135.04	H-Bond (Protein Donor)	false
O1B	N	GLY- 212	2.63	131.17	H-Bond (Protein Donor)	false
O1A	N	VAL- 213	2.91	163.16	H-Bond (Protein Donor)	false
O1B	N	TYR- 214	3.24	172.39	H-Bond (Protein Donor)	false
C1'	CB	PHE- 248	4.28	0	Hydrophobic	false
DuAr	DuAr	PHE- 248	3.67	0	Aromatic Face/Face	false
O2'	OE2	GLU- 252	2.51	155.85	H-Bond (Ligand Donor)	false