scPDB - 3t8v entry

Protein Data Bank Entry:

PDB ID : 3t8v

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-08-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	16.254
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.667	850.500

% Hydrophobic	% Polar
40.48	59.52
According to VolSite

Ligand :

HET Code:	BTJ
Formula:	C54H68N7O11
Molecular weight:	991.158 g/mol
DrugBank ID:	-
Buried Surface Area:	65.06 %
Polar Surface area:	281.21 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	8
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	33

Mass center Coordinates

X	Y	Z
14.7469	8.99852	15.5281

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
O11	ZN	ZN- 1	2.39	0	Metal Acceptor	false
N6	OE2	GLU- 319	3.91	0	Ionic (Ligand Cationic)	false
N6	OE1	GLU- 319	3.04	0	Ionic (Ligand Cationic)	false
N6	OE1	GLU- 319	3.04	168.61	H-Bond (Ligand Donor)	false
C44	CB	GLU- 319	3.76	0	Hydrophobic	false
C54	CB	ASN- 458	3.8	0	Hydrophobic	false
C5	CB	VAL- 459	3.65	0	Hydrophobic	false
C8	CG1	VAL- 459	4.3	0	Hydrophobic	false
C47	CG1	VAL- 459	4.44	0	Hydrophobic	false
C43	CG2	VAL- 459	3.95	0	Hydrophobic	false
C54	CG1	VAL- 459	3.66	0	Hydrophobic	false
O1	N	GLY- 460	2.69	135.51	H-Bond (Protein Donor)	false
O1	N	ALA- 461	3.23	148.56	H-Bond (Protein Donor)	false
C44	SD	MET- 462	3.45	0	Hydrophobic	false
N6	OE1	GLU- 463	3.63	0	Ionic (Ligand Cationic)	false
C1	CG2	VAL- 493	4.16	0	Hydrophobic	false
C1	CB	HIS- 496	4.35	0	Hydrophobic	false
N5	OE2	GLU- 497	2.74	155.14	H-Bond (Ligand Donor)	false
O11	OE1	GLU- 497	2.53	158.63	H-Bond (Ligand Donor)	false
O11	OE2	GLU- 497	3.3	140.02	H-Bond (Ligand Donor)	false
N6	OE2	GLU- 519	2.67	0	Ionic (Ligand Cationic)	false
N6	OE1	GLU- 519	3.94	0	Ionic (Ligand Cationic)	false
C51	CB	ALA- 572	3.87	0	Hydrophobic	false
C7	CB	TYR- 575	4.2	0	Hydrophobic	false
C8	CB	TYR- 575	3.74	0	Hydrophobic	false
C47	CB	TYR- 575	4.28	0	Hydrophobic	false
C49	CD1	TYR- 575	3.65	0	Hydrophobic	false
C51	CB	TYR- 575	3.92	0	Hydrophobic	false
C47	CD2	TYR- 575	3.27	0	Hydrophobic	false
C25	CG2	THR- 576	4.3	0	Hydrophobic	false
N6	OH	TYR- 580	3.4	140.06	H-Bond (Ligand Donor)	false
C7	CZ	TYR- 580	4.2	0	Hydrophobic	false
O9	OH	TYR- 580	2.81	141.4	H-Bond (Protein Donor)	false
C50	SD	MET- 1034	3.93	0	Hydrophobic	false
C53	CB	MET- 1034	3.65	0	Hydrophobic	false
C55	SD	MET- 1034	3.26	0	Hydrophobic	false
C11	CG2	THR- 1037	4.48	0	Hydrophobic	false
O4	NE2	GLN- 1038	3.19	130.69	H-Bond (Protein Donor)	false
C11	CG	GLN- 1038	4.31	0	Hydrophobic	false
C53	CG	GLN- 1038	4.4	0	Hydrophobic	false