scPDB - 4aub entry

Protein Data Bank Entry:

PDB ID : 4aub

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2012-05-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-glyceraldehyde 3-phosphate reductase
ID:	GPR_ECOLI
AC:	Q46851
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	32.086
Number of residues:	52
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.492	796.500

% Hydrophobic	% Polar
41.10	58.90
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	80.91 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-36.2973	27.7657	-21.3757

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
C3D	CE3	TRP- 33	4.13	0	Hydrophobic	false
C2D	CB	TRP- 33	3.51	0	Hydrophobic	false
O3D	N	TRP- 33	2.85	153.39	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 35	3.32	134.59	H-Bond (Protein Donor)	false
O2D	OD2	ASP- 61	2.66	144.26	H-Bond (Ligand Donor)	false
C2D	CZ	TYR- 66	3.82	0	Hydrophobic	false
N7N	OG	SER- 168	2.76	137.59	H-Bond (Ligand Donor)	false
N7N	OE1	GLN- 193	3.22	165.77	H-Bond (Ligand Donor)	false
C3N	CB	PHE- 222	4.34	0	Hydrophobic	false
DuAr	DuAr	PHE- 222	3.43	0	Aromatic Face/Face	false
C5N	CG2	THR- 223	3.86	0	Hydrophobic	false
O2A	N	LEU- 225	3.09	140.04	H-Bond (Protein Donor)	false
O2A	N	GLN- 227	2.81	143.32	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 243	3.55	0	Ionic (Protein Cationic)	false
O2N	CZ	ARG- 243	3.95	0	Ionic (Protein Cationic)	false
O1N	NH1	ARG- 243	3.47	129.61	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 243	2.76	171.27	H-Bond (Protein Donor)	false
O2N	NH1	ARG- 243	2.94	162.23	H-Bond (Protein Donor)	false
O1X	N	ARG- 243	3	161.05	H-Bond (Protein Donor)	false
C4D	CG	LEU- 299	3.87	0	Hydrophobic	false
C2D	CD2	LEU- 299	4.39	0	Hydrophobic	false
O1A	N	GLY- 301	3.4	162.72	H-Bond (Protein Donor)	false
O2X	OG	SER- 303	2.59	158.31	H-Bond (Protein Donor)	false
O2X	NE2	GLN- 307	2.87	171.38	H-Bond (Protein Donor)	false
N6A	OE1	GLU- 310	3.03	171.09	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 311	3.2	160.1	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 311	3.07	144.7	H-Bond (Ligand Donor)	false