scPDB - 5ab6 entry

Protein Data Bank Entry:

PDB ID : 5ab6

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-08-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nonspecific lipid-transfer protein, putative
ID:	C9ZUV7_TRYB9
AC:	C9ZUV7
Organism:	Trypanosoma brucei gambiense
Reign:	Eukaryota
TaxID:	679716
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	95 %
D	5 %

Ligand binding site composition:

B-Factor:	24.913
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.274	735.750

% Hydrophobic	% Polar
61.47	38.53
According to VolSite

Ligand :

HET Code:	CAA
Formula:	C25H36N7O18P3S
Molecular weight:	847.576 g/mol
DrugBank ID:	DB03059
Buried Surface Area:	51.91 %
Polar Surface area:	446.75 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
-38.9688	-28.3176	73.2494

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
C4	CZ	PHE- 59	4.27	0	Hydrophobic	false
O3	N	GLY- 87	2.9	156.31	H-Bond (Protein Donor)	false
O1A	OG	SER- 122	2.71	147.59	H-Bond (Protein Donor)	false
C6P	CZ	PHE- 125	3.75	0	Hydrophobic	false
CDP	CG	PRO- 141	4	0	Hydrophobic	false
S1P	CG2	ILE- 143	3.67	0	Hydrophobic	false
S1P	CE2	TYR- 147	4.19	0	Hydrophobic	false
O4A	NH1	ARG- 197	3.13	164	H-Bond (Protein Donor)	false
CDP	CG1	VAL- 199	3.96	0	Hydrophobic	false
CEP	CG2	VAL- 199	3.95	0	Hydrophobic	false
C1B	CD2	LEU- 205	4.34	0	Hydrophobic	false
CEP	CD1	LEU- 205	3.55	0	Hydrophobic	false
CEP	SG	CYS- 208	3.8	0	Hydrophobic	false
C6P	CB	ALA- 209	4.44	0	Hydrophobic	false
C2P	CB	ALA- 209	4.1	0	Hydrophobic	false
O1	OH	TYR- 297	2.62	162.64	H-Bond (Protein Donor)	false
C2	CE2	TYR- 297	3.99	0	Hydrophobic	false
C2P	CB	CYS- 299	3.59	0	Hydrophobic	false
C2P	CE2	PHE- 300	3.91	0	Hydrophobic	false
C4	CE3	TRP- 357	4.01	0	Hydrophobic	false
O3	N	GLY- 395	2.89	155.76	H-Bond (Protein Donor)	false