scPDB - 1yw9 entry

Protein Data Bank Entry:

PDB ID : 1yw9

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2005-02-17

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:	17.621
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.953	452.250

% Hydrophobic	% Polar
58.96	41.04
According to VolSite

Ligand :

HET Code:	A84
Formula:	C22H25FN2O4S
Molecular weight:	432.508 g/mol
DrugBank ID:	DB07323
Buried Surface Area:	60.49 %
Polar Surface area:	99.12 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.8691	30.2433	18.8388

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
C6	CB	PHE- 219	3.89	0	Hydrophobic	false
C21	CB	ALA- 230	4.21	0	Hydrophobic	false
O13	NE2	HIS- 231	2.94	176.26	H-Bond (Protein Donor)	false
F24	CD2	LEU- 328	3.39	0	Hydrophobic	false
C7	CG2	ILE- 338	3.57	0	Hydrophobic	false
C10	CG1	ILE- 338	3.91	0	Hydrophobic	false
C8	CB	HIS- 339	4.12	0	Hydrophobic	false
F24	CZ	PHE- 366	3.44	0	Hydrophobic	false
C1	CB	HIS- 382	4.38	0	Hydrophobic	false
C7	CE	MET- 384	3.69	0	Hydrophobic	false
C1	CB	ALA- 414	3.56	0	Hydrophobic	false
C2	CG	TYR- 444	3.81	0	Hydrophobic	false
C20	CD1	LEU- 447	3.61	0	Hydrophobic	false
O12	MN	MN- 481	2.2	0	Metal Acceptor	false