scPDB - 2wzm entry

Protein Data Bank Entry:

PDB ID : 2wzm

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2009-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346
ID:	Y2407_MYCS2
AC:	A0QV09
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.848
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.019	506.250

% Hydrophobic	% Polar
36.67	63.33
According to VolSite

Ligand :

HET Code:	NA7
Formula:	C15H20N5O16P3
Molecular weight:	619.264 g/mol
DrugBank ID:	-
Buried Surface Area:	60.87 %
Polar Surface area:	358.57 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
10.0794	45.6026	-5.65656

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
O3D	N	GLY- 196	2.92	172.46	H-Bond (Protein Donor)	false
O2N	N	LEU- 198	2.96	154.5	H-Bond (Protein Donor)	false
O1N	N	VAL- 200	2.59	147.53	H-Bond (Protein Donor)	false
C1B	CD1	LEU- 204	4.35	0	Hydrophobic	false
C3D	CG2	ILE- 236	4.19	0	Hydrophobic	false
O1A	NH2	ARG- 238	3.23	153.44	H-Bond (Protein Donor)	false
O2A	NE	ARG- 238	2.64	166.58	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 238	3.18	131.54	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 238	3.34	0	Ionic (Protein Cationic)	false
C1D	CD	ARG- 238	4.24	0	Hydrophobic	false
C5D	CB	ARG- 238	3.57	0	Hydrophobic	false
O3X	OG	SER- 239	2.54	164.22	H-Bond (Protein Donor)	false
O1X	N	ALA- 240	2.84	164.14	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 244	3.64	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 244	3.64	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 244	2.74	162.04	H-Bond (Protein Donor)	false
O3X	NE	ARG- 244	2.78	175.13	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 248	3.21	170.62	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 248	2.77	142.1	H-Bond (Ligand Donor)	false
O1A	NH2	ARG- 274	3.12	153.78	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 274	2.88	174.66	H-Bond (Protein Donor)	false
O5D	NH2	ARG- 274	3.48	122.17	H-Bond (Protein Donor)	false
O5D	NH1	ARG- 274	3.39	123.64	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 274	3.78	0	Ionic (Protein Cationic)	false
O2N	O	HOH- 2257	2.81	179.94	H-Bond (Protein Donor)	false