scPDB - 4fll entry

Protein Data Bank Entry:

PDB ID : 4fll

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-06-14

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:	15.936
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.587	330.750

% Hydrophobic	% Polar
55.10	44.90
According to VolSite

Ligand :

HET Code:	YZ6
Formula:	C25H35NO6
Molecular weight:	445.548 g/mol
DrugBank ID:	-
Buried Surface Area:	63.69 %
Polar Surface area:	112.16 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
20.2804	-3.50581	15.2953

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
C08	CB	PRO- 192	3.95	0	Hydrophobic	false
C08	CD2	TYR- 195	3.68	0	Hydrophobic	false
C09	CD1	PHE- 198	4.17	0	Hydrophobic	false
C09	SG	CYS- 203	3.55	0	Hydrophobic	false
C25	SG	CYS- 211	4.11	0	Hydrophobic	false
O6	NE2	HIS- 212	2.86	153.26	H-Bond (Protein Donor)	false
C09	CB	HIS- 212	4.39	0	Hydrophobic	false
O1	OG1	THR- 231	3.48	127.21	H-Bond (Ligand Donor)	false
C25	CB	TYR- 300	3.77	0	Hydrophobic	false
N	O	CYS- 301	2.82	137.16	H-Bond (Ligand Donor)	false
C21	SG	CYS- 301	4.03	0	Hydrophobic	false
C20	CB	CYS- 301	3.76	0	Hydrophobic	false
C13	CB	HIS- 303	4.33	0	Hydrophobic	false
C04	CZ	PHE- 309	3.96	0	Hydrophobic	false
C08	CE2	PHE- 309	3.85	0	Hydrophobic	false
O2	NE2	HIS- 310	2.67	167.63	H-Bond (Ligand Donor)	false
O3	OE2	GLU- 336	2.54	151.81	H-Bond (Ligand Donor)	false
C25	SD	MET- 338	3.98	0	Hydrophobic	false
C10	CZ3	TRP- 353	3.82	0	Hydrophobic	false
O2	MN	MN- 501	2.27	0	Metal Acceptor	false
O3	MN	MN- 501	2.19	0	Metal Acceptor	false
O3	MN	MN- 502	2.28	0	Metal Acceptor	false
O1	MN	MN- 502	2.18	0	Metal Acceptor	false
O1	O	HOH- 663	2.61	144.85	H-Bond (Ligand Donor)	false