scPDB - 3wfj entry

Protein Data Bank Entry:

PDB ID : 3wfj

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2013-07-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-dehydropantoate 2-reductase
ID:	E3USM3_ENTFC
AC:	E3USM3
Organism:	Enterococcus faecium
Reign:	Bacteria
TaxID:	1352
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.700
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.010	1528.875

% Hydrophobic	% Polar
44.15	55.85
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	62.75 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
27.3947	13.773	115.429

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
O2N	N	MET- 11	2.64	168.2	H-Bond (Protein Donor)	false
C5D	CB	MET- 11	4.11	0	Hydrophobic	false
C5N	CE	MET- 11	3.64	0	Hydrophobic	false
C3N	SD	MET- 11	4.31	0	Hydrophobic	false
O3B	OD1	ASP- 30	2.61	139.23	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 30	2.67	156.55	H-Bond (Ligand Donor)	false
C1B	CE3	TRP- 32	4.47	0	Hydrophobic	false
C4D	CD1	PHE- 77	3.69	0	Hydrophobic	false
O1A	NZ	LYS- 79	3	146.03	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 79	3	0	Ionic (Protein Cationic)	false
C3D	CD	LYS- 79	3.92	0	Hydrophobic	false
O4B	NE2	GLN- 82	3.25	156.64	H-Bond (Protein Donor)	false
C3D	CD1	LEU- 104	4.07	0	Hydrophobic	false
O3D	N	ASN- 105	3.43	159.41	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 105	3.47	142.93	H-Bond (Protein Donor)	false
C2D	CB	ASN- 105	4.4	0	Hydrophobic	false
C5N	CG2	THR- 127	4.41	0	Hydrophobic	false
O7N	N	ALA- 131	2.67	141.6	H-Bond (Protein Donor)	false
N7N	O	ALA- 131	2.72	147.89	H-Bond (Ligand Donor)	false
C2B	CD2	LEU- 133	4.38	0	Hydrophobic	false
O1A	CZ	ARG- 270	3.26	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 270	2.92	139.55	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 270	2.75	148.61	H-Bond (Protein Donor)	false
O3D	OE2	GLU- 273	2.77	161.72	H-Bond (Ligand Donor)	false
O2D	OE1	GLU- 273	2.54	145.45	H-Bond (Ligand Donor)	false