scPDB - 1qzy entry

Protein Data Bank Entry:

PDB ID : 1qzy

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2003-09-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine aminopeptidase 2
ID:	MAP2_HUMAN
AC:	P50579
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.717
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.876	502.875

% Hydrophobic	% Polar
46.31	53.69
According to VolSite

Ligand :

HET Code:	TDE
Formula:	C18H32N2O7
Molecular weight:	388.456 g/mol
DrugBank ID:	DB03396
Buried Surface Area:	66.63 %
Polar Surface area:	148.35 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
17.2183	29.2708	18.8854

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
C15	CE1	PHE- 219	4.22	0	Hydrophobic	false
C20	CB	PHE- 219	3.71	0	Hydrophobic	false
C25	CB	ALA- 230	3.99	0	Hydrophobic	false
O21	NE2	HIS- 231	2.96	141.36	H-Bond (Protein Donor)	false
O11	NE2	HIS- 231	3.21	123.77	H-Bond (Protein Donor)	false
C25	CD2	LEU- 328	3.55	0	Hydrophobic	false
O8	N	ASN- 329	2.86	147.91	H-Bond (Protein Donor)	false
O8	ND2	ASN- 329	3.27	160.97	H-Bond (Protein Donor)	false
C4	CB	ASN- 329	4.49	0	Hydrophobic	false
N9	O	ASN- 329	3.06	150.42	H-Bond (Ligand Donor)	false
C4	CB	HIS- 331	3.79	0	Hydrophobic	false
C21	CG2	ILE- 338	4.32	0	Hydrophobic	false
C5	CB	HIS- 339	4.47	0	Hydrophobic	false
O22	NE2	HIS- 339	2.67	139.17	H-Bond (Ligand Donor)	false
O7	OG1	THR- 343	2.91	166.5	H-Bond (Ligand Donor)	false
O23	OE1	GLU- 364	2.67	149.11	H-Bond (Ligand Donor)	false
C25	CZ	PHE- 366	3.58	0	Hydrophobic	false
C19	CB	HIS- 382	4.47	0	Hydrophobic	false
C21	CE	MET- 384	4.28	0	Hydrophobic	false
C20	CB	ALA- 414	3.41	0	Hydrophobic	false
C21	CD2	TYR- 444	4.07	0	Hydrophobic	false
C19	CB	TYR- 444	4.1	0	Hydrophobic	false