scPDB - 2b4r entry

Protein Data Bank Entry:

PDB ID : 2b4r

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2005-09-26

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
ID:	Q8T6B1_PLAFA
AC:	Q8T6B1
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	5833
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	61.466
Number of residues:	14
Including
Standard Amino Acids:	11
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.158	1059.750

% Hydrophobic	% Polar
35.03	64.97
According to VolSite

Ligand :

HET Code:	AES
Formula:	C8H11FNO2S
Molecular weight:	204.242 g/mol
DrugBank ID:	DB07347
Buried Surface Area:	48.76 %
Polar Surface area:	70.16 Å2

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

Mass center Coordinates

X	Y	Z
13.7888	17.0125	11.8252

Binding mode :

What is Poseview ?

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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
C2	CB	THR- 183	4.04	0	Hydrophobic	false
O1S	OG1	THR- 183	3.15	154.78	H-Bond (Protein Donor)	false
C3	CB	ALA- 184	4.09	0	Hydrophobic	false
C6	CB	ASN- 185	4.08	0	Hydrophobic	false
F	C2D	NAD- 801	4.44	0	Hydrophobic	false
C5	C3D	NAD- 801	3.96	0	Hydrophobic	false
C1	C2D	NAD- 801	3.5	0	Hydrophobic	false
O2S	O2D	NAD- 801	2.82	170.08	H-Bond (Protein Donor)	false
N8	O1A	NAD- 801	2.6	159.18	H-Bond (Ligand Donor)	false
N8	O1A	NAD- 801	2.6	0	Ionic (Ligand Cationic)	false