scPDB - 2vyn entry

Protein Data Bank Entry:

PDB ID : 2vyn

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-07-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyceraldehyde-3-phosphate dehydrogenase A
ID:	G3P1_ECOLI
AC:	P0A9B2
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	91 %
C	9 %

Ligand binding site composition:

B-Factor:	21.602
Number of residues:	52
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.240	945.000

% Hydrophobic	% Polar
46.07	53.93
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	62.11 %
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
17.8389	30.1825	13.9803

Binding mode :

What is Poseview ?

2D View
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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
O2A	N	ARG- 10	2.97	158.68	H-Bond (Protein Donor)	false
O1N	N	ILE- 11	2.89	175.27	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 11	3.47	0	Hydrophobic	false
O3B	OD2	ASP- 32	2.82	167.65	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 32	3.45	129.39	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 32	2.63	174.93	H-Bond (Ligand Donor)	false
N6A	O	ARG- 76	3.01	175.66	H-Bond (Ligand Donor)	false
O4D	OG1	THR- 118	3.1	161.05	H-Bond (Protein Donor)	false
C5N	CB	CSD- 148	3.74	0	Hydrophobic	false
C3B	CG	PRO- 187	4.18	0	Hydrophobic	false
O7N	ND2	ASN- 312	2.58	168.71	H-Bond (Protein Donor)	false
C5N	CD2	TYR- 316	3.41	0	Hydrophobic	false
C5N	CB	TYR- 316	4.1	0	Hydrophobic	false
O3D	O	HOH- 2054	3.14	179.98	H-Bond (Protein Donor)	false
N1A	O	HOH- 2209	2.63	179.96	H-Bond (Protein Donor)	false
O1N	O	HOH- 2211	2.76	179.97	H-Bond (Protein Donor)	false