scPDB - 2gg8 entry

Protein Data Bank Entry:

PDB ID : 2gg8

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine aminopeptidase
ID:	MAP1_ECOLI
AC:	P0AE18
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.769
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.497	442.125

% Hydrophobic	% Polar
41.98	58.02
According to VolSite

Ligand :

HET Code:	U15
Formula:	C20H32N3O5
Molecular weight:	394.485 g/mol
DrugBank ID:	DB08669
Buried Surface Area:	60.8 %
Polar Surface area:	132.37 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-3.05343	-1.91761	7.89043

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
C6	SG	CYS- 59	4.1	0	Hydrophobic	false
C48	CE2	TYR- 62	3.93	0	Hydrophobic	false
C53	CD2	TYR- 62	3.33	0	Hydrophobic	false
C9	CD2	TYR- 62	4.09	0	Hydrophobic	false
C51	CB	HIS- 63	4.2	0	Hydrophobic	false
C9	CB	TYR- 65	4.04	0	Hydrophobic	false
C2	SG	CYS- 70	3.49	0	Hydrophobic	false
O35	NE2	HIS- 79	2.75	130.44	H-Bond (Protein Donor)	false
N15	OG1	THR- 99	3.04	154.08	H-Bond (Ligand Donor)	false
C44	CD1	TYR- 168	3.59	0	Hydrophobic	false
C28	CB	TYR- 168	4.41	0	Hydrophobic	false
C7	CZ	PHE- 177	3.69	0	Hydrophobic	false
C1	CZ	PHE- 177	3.26	0	Hydrophobic	false
O22	NE2	HIS- 178	2.73	159.83	H-Bond (Protein Donor)	false
C51	CZ3	TRP- 221	3.71	0	Hydrophobic	false
C9	CZ3	TRP- 221	3.67	0	Hydrophobic	false