scPDB - 2nm2 entry

Protein Data Bank Entry:

PDB ID : 2nm2

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-10-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroneopterin aldolase
ID:	FOLB_STAAU
AC:	P56740
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	66 %
B	31 %
C	3 %

Ligand binding site composition:

B-Factor:	27.265
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.761	391.500

% Hydrophobic	% Polar
56.03	43.97
According to VolSite

Ligand :

HET Code:	NEU
Formula:	C9H11N5O4
Molecular weight:	253.215 g/mol
DrugBank ID:	-
Buried Surface Area:	77.4 %
Polar Surface area:	153.94 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
44.9089	47.9342	26.4553

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
C16	CB	ALA- 18	4.36	0	Hydrophobic	false
O21	N	ALA- 18	2.98	156.77	H-Bond (Protein Donor)	false
O21	OE1	GLU- 22	3.44	130.32	H-Bond (Ligand Donor)	false
O21	OE2	GLU- 22	2.76	164.4	H-Bond (Ligand Donor)	false
N13	O	VAL- 52	2.62	148.94	H-Bond (Ligand Donor)	false
N4	N	TYR- 54	2.85	165.84	H-Bond (Protein Donor)	false
O22	OH	TYR- 54	2.59	145.34	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 54	3.76	0	Aromatic Face/Face	false
C28	CE1	TYR- 54	4.46	0	Hydrophobic	false
O11	N	LEU- 73	2.62	160.97	H-Bond (Protein Donor)	false
N2	OE1	GLU- 74	3.02	144.45	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 74	3.03	133.28	H-Bond (Ligand Donor)	false
N13	OE2	GLU- 74	3	138.92	H-Bond (Ligand Donor)	false
C26	CE	LYS- 100	4.34	0	Hydrophobic	false
C28	CB	PRO- 103	3.49	0	Hydrophobic	false
O24	O	PRO- 104	3.31	121.33	H-Bond (Ligand Donor)	false
C28	CG	PRO- 104	3.7	0	Hydrophobic	false
C28	CG1	ILE- 105	3.93	0	Hydrophobic	false