scPDB - 1m4d entry

Protein Data Bank Entry:

PDB ID : 1m4d

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2002-07-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminoglycoside 2'-N-acetyltransferase
ID:	AAC2_MYCTU
AC:	P9WQG9
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	26.129
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.539	850.500

% Hydrophobic	% Polar
39.29	60.71
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	42.72 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
-11.3916	33.5421	48.329

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
C6P	CZ	PHE- 32	3.79	0	Hydrophobic	false
C2P	CZ	PHE- 32	4.23	0	Hydrophobic	false
CEP	CG1	VAL- 84	4.02	0	Hydrophobic	false
C2P	CB	VAL- 84	3.64	0	Hydrophobic	false
N4P	O	VAL- 84	2.73	166.46	H-Bond (Ligand Donor)	false
CEP	CG2	VAL- 86	3.94	0	Hydrophobic	false
CAP	CB	VAL- 86	4.37	0	Hydrophobic	false
O9P	N	VAL- 86	2.8	173.52	H-Bond (Protein Donor)	false
CAP	CD	ARG- 91	3.85	0	Hydrophobic	false
O5A	N	GLY- 92	2.94	162.83	H-Bond (Protein Donor)	false
O2A	N	ARG- 94	2.73	146.11	H-Bond (Protein Donor)	false
O4A	N	VAL- 96	2.97	158.05	H-Bond (Protein Donor)	false
CCP	CB	VAL- 96	3.95	0	Hydrophobic	false
CEP	CG2	VAL- 96	3.91	0	Hydrophobic	false
S1P	CB	ALA- 122	4.35	0	Hydrophobic	false
O3B	NH2	ARG- 124	2.59	163.44	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 124	3.35	130.98	H-Bond (Protein Donor)	false
O7A	NH1	ARG- 124	2.84	152.23	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 124	3.53	0	Ionic (Protein Cationic)	false
S1P	CE2	TYR- 126	4.08	0	Hydrophobic	false
O4A	O	HOH- 609	2.53	133.78	H-Bond (Protein Donor)	false