scPDB - 3q44 entry

Protein Data Bank Entry:

PDB ID : 3q44

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:	6.310	6.310	6.310	0.000	6.310	1

List of CHEMBLId :

CHEMBL1614912

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:	13.797
Number of residues:	43
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.305	2288.250

% Hydrophobic	% Polar
42.48	57.52
According to VolSite

Ligand :

HET Code:	D50
Formula:	C23H30N2O5
Molecular weight:	414.495 g/mol
DrugBank ID:	-
Buried Surface Area:	68.49 %
Polar Surface area:	126.33 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
13.6074	10.1993	14.5739

Binding mode :

What is Poseview ?

2D View
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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
O2	ZN	ZN- 1	1.96	0	Metal Acceptor	false
N2	OE2	GLU- 319	3.82	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 319	2.77	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 319	2.77	156.96	H-Bond (Ligand Donor)	false
C21	CG	GLU- 319	3.99	0	Hydrophobic	false
C22	CB	GLU- 319	3.81	0	Hydrophobic	false
C12	CG1	VAL- 459	3.95	0	Hydrophobic	false
C11	CG2	VAL- 459	3.67	0	Hydrophobic	false
O4	N	GLY- 460	2.67	136.81	H-Bond (Protein Donor)	false
O5	N	GLY- 460	3.31	128.78	H-Bond (Protein Donor)	false
O4	N	ALA- 461	3.06	154.6	H-Bond (Protein Donor)	false
C22	SD	MET- 462	3.85	0	Hydrophobic	false
N2	OE2	GLU- 463	3.29	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 463	2.67	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 463	2.67	154.74	H-Bond (Ligand Donor)	false
C1	CG2	THR- 492	3.56	0	Hydrophobic	false
C1	CG2	VAL- 493	3.93	0	Hydrophobic	false
C4	CG2	VAL- 493	4.21	0	Hydrophobic	false
C1	CB	HIS- 496	3.47	0	Hydrophobic	false
N1	OE2	GLU- 497	2.88	167.19	H-Bond (Ligand Donor)	false
O2	OE1	GLU- 497	2.53	147.67	H-Bond (Ligand Donor)	false
O2	OE2	GLU- 497	3.24	140.64	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 519	2.98	162.52	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 519	2.98	0	Ionic (Ligand Cationic)	false
C3	CG2	VAL- 523	4.26	0	Hydrophobic	false
C17	CB	MET- 571	3.63	0	Hydrophobic	false
C18	CG	GLU- 572	3.83	0	Hydrophobic	false
C12	CB	TYR- 575	4.34	0	Hydrophobic	false
C14	CD1	TYR- 575	3.77	0	Hydrophobic	false
C20	CB	TYR- 575	3.86	0	Hydrophobic	false
C12	CD2	TYR- 575	3.39	0	Hydrophobic	false
O1	OH	TYR- 580	2.56	144.12	H-Bond (Protein Donor)	false
C3	CE1	TYR- 580	4	0	Hydrophobic	false
C16	SD	MET- 1034	3.86	0	Hydrophobic	false
C17	CG	MET- 1034	3.8	0	Hydrophobic	false
O5	O	HOH- 1389	2.67	162.34	H-Bond (Protein Donor)	false