scPDB - 2nq7 entry

Protein Data Bank Entry:

PDB ID : 2nq7

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2006-10-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine aminopeptidase 1
ID:	MAP11_HUMAN
AC:	P53582
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:	17.202
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.771	567.000

% Hydrophobic	% Polar
41.07	58.93
According to VolSite

Ligand :

HET Code:	HM5
Formula:	C14H16N4O2S
Molecular weight:	304.367 g/mol
DrugBank ID:	DB07903
Buried Surface Area:	49.13 %
Polar Surface area:	112.21 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
13.458	31.5671	21.358

Binding mode :

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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
C12	CE2	TYR- 195	3.87	0	Hydrophobic	false
C14	CE2	TYR- 195	4.39	0	Hydrophobic	false
S	CD2	TYR- 195	3.48	0	Hydrophobic	false
C12	CD1	TYR- 196	3.99	0	Hydrophobic	false
C14	CE1	TYR- 196	3.67	0	Hydrophobic	false
DuAr	DuAr	HIS- 310	3.83	0	Aromatic Face/Face	false
DuAr	DuAr	HIS- 310	3.83	0	Aromatic Face/Face	false
C12	CH2	TRP- 353	3.76	0	Hydrophobic	false
S	CZ3	TRP- 353	3.46	0	Hydrophobic	false