scPDB - 1r58 entry

Protein Data Bank Entry:

PDB ID : 1r58

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2003-10-09

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:	16.004
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.868	398.250

% Hydrophobic	% Polar
58.47	41.53
According to VolSite

Ligand :

HET Code:	AO5
Formula:	C15H23ClN3O3S
Molecular weight:	360.879 g/mol
DrugBank ID:	DB07377
Buried Surface Area:	60.64 %
Polar Surface area:	131.37 Å2

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

Mass center Coordinates

X	Y	Z
17.6365	30.9432	17.197

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
S4	CB	PHE- 219	3.87	0	Hydrophobic	false
C5	CG	PHE- 219	3.58	0	Hydrophobic	false
C6	CD2	PHE- 219	4.24	0	Hydrophobic	false
C7	CE2	PHE- 219	4.23	0	Hydrophobic	false
N13	NE2	HIS- 231	2.64	145.94	H-Bond (Ligand Donor)	false
O12	NE2	HIS- 339	3.18	151.68	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 339	3.77	0	Aromatic Face/Face	false
CL23	CB	HIS- 339	3.74	0	Hydrophobic	false
O10	OE2	GLU- 364	2.73	133.93	H-Bond (Ligand Donor)	false
C3	CB	HIS- 382	4.37	0	Hydrophobic	false
C2	SD	MET- 384	3.74	0	Hydrophobic	false
CL23	CE	MET- 384	4.02	0	Hydrophobic	false
C2	CB	ALA- 414	3.6	0	Hydrophobic	false
C1	CG	TYR- 444	4.46	0	Hydrophobic	false
C2	CD2	TYR- 444	3.93	0	Hydrophobic	false
C3	CB	TYR- 444	3.5	0	Hydrophobic	false
CL23	CZ	TYR- 444	4.34	0	Hydrophobic	false
O10	MN	MN- 480	2.29	0	Metal Acceptor	false
O10	MN	MN- 481	2.34	0	Metal Acceptor	false
O12	MN	MN- 481	2.49	0	Metal Acceptor	false
O10	O	HOH- 744	3.18	120.13	H-Bond (Ligand Donor)	false