scPDB - 4zm6 entry

Protein Data Bank Entry:

PDB ID : 4zm6

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2015-05-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acetyl-beta-D glucosaminidase
ID:	V9M3A9_RHIMI
AC:	V9M3A9
Organism:	Rhizomucor miehei
Reign:	Eukaryota
TaxID:	4839
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	64.135
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.245	631.125

% Hydrophobic	% Polar
57.22	42.78
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	52.38 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
107.783	177.026	150.436

Binding mode :

What is Poseview ?

2D View
3D View

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
N3A	NH2	ARG- 520	3.33	120.62	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 520	3.84	163	Pi/Cation	false
C6P	CG2	ILE- 560	3.86	0	Hydrophobic	false
C6P	CZ	PHE- 561	3.81	0	Hydrophobic	false
CDP	CD1	LEU- 616	4.21	0	Hydrophobic	false
N4P	O	LEU- 616	3.05	169.41	H-Bond (Ligand Donor)	false
O	N	LEU- 616	2.94	137.71	H-Bond (Protein Donor)	false
CDP	CG1	VAL- 618	4.12	0	Hydrophobic	false
O9P	N	VAL- 618	3.24	169.2	H-Bond (Protein Donor)	false
CAP	CG	GLN- 623	3.93	0	Hydrophobic	false
O5A	N	GLY- 624	3.16	147.98	H-Bond (Protein Donor)	false
O1A	N	GLY- 626	2.83	151.75	H-Bond (Protein Donor)	false
O4A	N	GLY- 628	2.9	152.97	H-Bond (Protein Donor)	false
O2A	N	THR- 629	3.01	142.67	H-Bond (Protein Donor)	false
O2A	OG1	THR- 629	2.51	153.95	H-Bond (Protein Donor)	false
S1P	CD2	PHE- 657	4.26	0	Hydrophobic	false
C2P	CG1	VAL- 660	4.09	0	Hydrophobic	false
CEP	CB	ALA- 670	3.76	0	Hydrophobic	false
C2P	CB	ALA- 670	4.42	0	Hydrophobic	false
C5B	CD2	PHE- 673	4.49	0	Hydrophobic	false
CCP	CE2	PHE- 673	3.68	0	Hydrophobic	false
CEP	CG	PHE- 673	4.17	0	Hydrophobic	false
C2P	CE2	PHE- 674	3.95	0	Hydrophobic	false
O7A	NZ	LYS- 676	2.75	170.33	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 676	2.75	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 676	3.4	0	Ionic (Protein Cationic)	false
O4A	O	HOH- 1005	2.76	165.12	H-Bond (Protein Donor)	false