scPDB - 3pkd entry

Protein Data Bank Entry:

PDB ID : 3pkd

Resolution :1.470 Å

Experimental Method : X-ray

Deposition Date : 2010-11-11

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:	MAP12_MYCTU
AC:	P9WK19
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.104
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.604	513.000

% Hydrophobic	% Polar
44.74	55.26
According to VolSite

Ligand :

HET Code:	Y10
Formula:	C21H31NO5
Molecular weight:	377.475 g/mol
DrugBank ID:	-
Buried Surface Area:	63.37 %
Polar Surface area:	99.02 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
25.7977	-1.60767	11.098

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
C10	CG2	THR- 94	3.95	0	Hydrophobic	false
C09	CE2	TYR- 97	3.83	0	Hydrophobic	false
C10	CD2	TYR- 97	3.41	0	Hydrophobic	false
C08	CD1	PHE- 100	4.34	0	Hydrophobic	false
C08	SG	CYS- 105	3.62	0	Hydrophobic	false
C21	SG	CYS- 113	4.07	0	Hydrophobic	false
O4	NE2	HIS- 114	3.02	123.62	H-Bond (Protein Donor)	false
O5	NE2	HIS- 114	2.88	154.7	H-Bond (Protein Donor)	false
C21	CB	PHE- 202	4.08	0	Hydrophobic	false
N	O	THR- 203	3.08	133.58	H-Bond (Ligand Donor)	false
C17	CB	HIS- 205	4.23	0	Hydrophobic	false
C04	CZ	PHE- 211	3.84	0	Hydrophobic	false
C10	CE2	PHE- 211	4.02	0	Hydrophobic	false
O2	NE2	HIS- 212	2.67	171.96	H-Bond (Ligand Donor)	false
C20	CB	HIS- 212	3.6	0	Hydrophobic	false
C17	CG2	VAL- 216	4.17	0	Hydrophobic	false
O3	OE1	GLU- 238	2.51	162.05	H-Bond (Ligand Donor)	false
C21	SD	MET- 240	3.88	0	Hydrophobic	false
C09	CZ3	TRP- 255	3.78	0	Hydrophobic	false
O2	MN	MN- 286	2.37	0	Metal Acceptor	false
O3	MN	MN- 286	2.17	0	Metal Acceptor	false
O1	MN	MN- 287	2.14	0	Metal Acceptor	false
O3	MN	MN- 287	2.26	0	Metal Acceptor	false