scPDB - 3q43 entry

Protein Data Bank Entry:

PDB ID : 3q43

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.370	7.370	7.370	0.000	7.370	1

List of CHEMBLId :

CHEMBL1614913

Binding Site :

Uniprot Annotation

Name:	M1 family aminopeptidase
ID:	AMP1_PLAFQ
AC:	O96935
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	186763
EC Number:	3.4.11

Chains:

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

Ligand binding site composition:

B-Factor:	13.775
Number of residues:	38
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.085	1019.250

% Hydrophobic	% Polar
42.38	57.62
According to VolSite

Ligand :

HET Code:	D66
Formula:	C17H26N2O5
Molecular weight:	338.399 g/mol
DrugBank ID:	-
Buried Surface Area:	67.65 %
Polar Surface area:	126.33 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
14.8216	10.7664	12.9604

Binding mode :

What is Poseview ?

2D View
3D View

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
O2	ZN	ZN- 1	1.96	0	Metal Acceptor	false
N1	OE2	GLU- 319	3.84	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 319	2.81	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 319	2.81	151.96	H-Bond (Ligand Donor)	false
C4	CB	GLU- 319	3.93	0	Hydrophobic	false
C16	CG2	VAL- 459	4.09	0	Hydrophobic	false
C17	CG1	VAL- 459	4.17	0	Hydrophobic	false
C5	CG2	VAL- 459	3.92	0	Hydrophobic	false
O4	N	GLY- 460	3.24	127.11	H-Bond (Protein Donor)	false
O5	N	GLY- 460	2.59	136.76	H-Bond (Protein Donor)	false
O5	N	ALA- 461	3.07	151.37	H-Bond (Protein Donor)	false
C6	SD	MET- 462	3.85	0	Hydrophobic	false
N1	OE2	GLU- 463	3.55	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 463	2.82	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 463	2.82	161.94	H-Bond (Ligand Donor)	false
O4	NH2	ARG- 489	3.32	155.1	H-Bond (Protein Donor)	false
C14	CG2	THR- 492	3.54	0	Hydrophobic	false
C11	CG2	VAL- 493	4.24	0	Hydrophobic	false
C14	CG2	VAL- 493	3.85	0	Hydrophobic	false
C14	CB	HIS- 496	3.63	0	Hydrophobic	false
N2	OE2	GLU- 497	2.9	167.68	H-Bond (Ligand Donor)	false
O2	OE1	GLU- 497	2.66	152.1	H-Bond (Ligand Donor)	false
O2	OE2	GLU- 497	3.35	138.96	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 519	2.97	169.55	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 519	2.97	0	Ionic (Ligand Cationic)	false
C13	CG2	VAL- 523	4.45	0	Hydrophobic	false
C1	CB	GLU- 572	4.21	0	Hydrophobic	false
C1	CD1	TYR- 575	3.66	0	Hydrophobic	false
C17	CB	TYR- 575	4.1	0	Hydrophobic	false
C17	CD2	TYR- 575	3.19	0	Hydrophobic	false
O3	OH	TYR- 580	2.7	141.36	H-Bond (Protein Donor)	false
C13	CE1	TYR- 580	4.16	0	Hydrophobic	false
O4	O	HOH- 1220	2.73	159.18	H-Bond (Protein Donor)	false