scPDB - 3t8w entry

Protein Data Bank Entry:

PDB ID : 3t8w

Resolution :2.000 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:	M17 leucyl aminopeptidase
ID:	Q8IL11_PLAF7
AC:	Q8IL11
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
H	86 %
I	2 %
K	12 %

Ligand binding site composition:

B-Factor:	18.623
Number of residues:	53
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	3
Water Molecules:	2
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.499	664.875

% Hydrophobic	% Polar
36.04	63.96
According to VolSite

Ligand :

HET Code:	DGZ
Formula:	C57H68N7O10
Molecular weight:	1011.191 g/mol
DrugBank ID:	-
Buried Surface Area:	50.86 %
Polar Surface area:	271.98 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	8
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	32

Mass center Coordinates

X	Y	Z
101.93	58.9676	129.653

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
O8	NZ	LYS- 386	2.91	140.16	H-Bond (Protein Donor)	false
C10	CB	ALA- 388	3.74	0	Hydrophobic	false
N1	O	GLY- 390	3.07	136.25	H-Bond (Ligand Donor)	false
C5	CE	MET- 392	3.47	0	Hydrophobic	false
C23	CE	MET- 392	3.34	0	Hydrophobic	false
C54	CE	MET- 392	3.53	0	Hydrophobic	false
C54	CE	MET- 396	3.67	0	Hydrophobic	false
C53	CZ	PHE- 398	3.47	0	Hydrophobic	false
C39	CB	ASN- 457	3.74	0	Hydrophobic	false
C38	CB	ALA- 460	3.78	0	Hydrophobic	false
N6	O	THR- 486	3.4	153.6	H-Bond (Ligand Donor)	false
N5	O	LEU- 487	3.01	146.45	H-Bond (Ligand Donor)	false
O7	N	GLY- 489	3.04	156.25	H-Bond (Protein Donor)	false
C22	CD1	LEU- 492	3.9	0	Hydrophobic	false
C54	CD1	LEU- 492	4.47	0	Hydrophobic	false
C14	CZ	TYR- 493	4.27	0	Hydrophobic	false
C27	CE2	TYR- 493	3.27	0	Hydrophobic	false
C41	CD1	ILE- 547	3.73	0	Hydrophobic	false
C40	CG2	ILE- 547	4.23	0	Hydrophobic	false
C27	CB	VAL- 551	4.3	0	Hydrophobic	false
C30	CB	VAL- 551	4.32	0	Hydrophobic	false
C44	CB	SER- 554	4.16	0	Hydrophobic	false
C46	CB	SER- 554	4.22	0	Hydrophobic	false
C52	CB	ALA- 577	3.74	0	Hydrophobic	false
O9	ZN	ZN- 613	2.05	0	Metal Acceptor	false
O9	ZN	ZN- 614	2.2	0	Metal Acceptor	false
O7	O	HOH- 656	2.55	129.79	H-Bond (Protein Donor)	false