scPDB - 1r5h entry

Protein Data Bank Entry:

PDB ID : 1r5h

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2003-10-10

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:	14.698
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.750	455.625

% Hydrophobic	% Polar
54.81	45.19
According to VolSite

Ligand :

HET Code:	AO2
Formula:	C17H28N3O2
Molecular weight:	306.423 g/mol
DrugBank ID:	DB03086
Buried Surface Area:	65.42 %
Polar Surface area:	89 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
18.0065	29.3596	18.203

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
C7	CD2	PHE- 219	4.32	0	Hydrophobic	false
C8	CE2	PHE- 219	4.42	0	Hydrophobic	false
O13	NE2	HIS- 231	2.82	160.55	H-Bond (Protein Donor)	false
C22	CD2	LEU- 328	4.2	0	Hydrophobic	false
C20	CD2	LEU- 328	3.44	0	Hydrophobic	false
N15	NE2	HIS- 331	3.32	123.14	H-Bond (Ligand Donor)	false
C4	CG2	ILE- 338	3.44	0	Hydrophobic	false
O11	OE2	GLU- 364	2.63	150.67	H-Bond (Ligand Donor)	false
N14	OE1	GLU- 364	2.6	137.29	H-Bond (Ligand Donor)	false
C2	CB	HIS- 382	4.35	0	Hydrophobic	false
C4	CE	MET- 384	3.7	0	Hydrophobic	false
C2	CB	ALA- 414	3.75	0	Hydrophobic	false
C2	CG	TYR- 444	3.98	0	Hydrophobic	false
C3	CD1	TYR- 444	3.71	0	Hydrophobic	false
O11	MN	MN- 480	2.26	0	Metal Acceptor	false
O11	MN	MN- 481	2.36	0	Metal Acceptor	false