scPDB - 2esd entry

Protein Data Bank Entry:

PDB ID : 2esd

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2005-10-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
ID:	GAPN_STRMU
AC:	Q59931
Organism:	Streptococcus mutans serotype c
Reign:	Bacteria
TaxID:	210007
EC Number:	1.2.1.9

Chains:

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

Ligand binding site composition:

B-Factor:	28.000
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.121	796.500

% Hydrophobic	% Polar
55.93	44.07
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	45.35 %
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
-159.894	22.9302	38.2816

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
C4B	CG2	ILE- 150	4.43	0	Hydrophobic	false
C1B	CG2	ILE- 150	4.14	0	Hydrophobic	false
O3X	NZ	LYS- 177	2.93	151	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 177	2.93	0	Ionic (Protein Cationic)	false
C3B	CB	PRO- 179	4.29	0	Hydrophobic	false
O2X	N	THR- 180	2.75	153.7	H-Bond (Protein Donor)	false
O3X	OG1	THR- 180	2.54	156.09	H-Bond (Protein Donor)	false
O3X	N	THR- 180	3.26	135.07	H-Bond (Protein Donor)	false
O3X	N	GLY- 210	3.12	152.39	H-Bond (Protein Donor)	false
N6A	OD2	ASP- 215	2.75	152.65	H-Bond (Ligand Donor)	false
C5B	CZ	PHE- 228	3.67	0	Hydrophobic	false
C4B	CE1	PHE- 228	3.58	0	Hydrophobic	false
C1B	CE1	PHE- 228	4.34	0	Hydrophobic	false
O1A	OG	SER- 231	2.66	144.24	H-Bond (Protein Donor)	false
C3N	CB	SER- 231	3.63	0	Hydrophobic	false
O7N	N	GLY- 233	2.91	122.3	H-Bond (Protein Donor)	false
C5B	CG1	ILE- 234	3.77	0	Hydrophobic	false
O3D	NZ	LYS- 329	2.84	130.3	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 329	2.63	155.83	H-Bond (Protein Donor)	false