scPDB - 1ky8 entry

Protein Data Bank Entry:

PDB ID : 1ky8

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2002-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
ID:	GAPN_THETE
AC:	O57693
Organism:	Thermoproteus tenax
Reign:	Archaea
TaxID:	2271
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.546
Number of residues:	56
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.905	931.500

% Hydrophobic	% Polar
45.29	54.71
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	70.5 %
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
-19.5358	61.2647	12.6564

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- 164	3.75	0	Hydrophobic	false
C1B	CG2	ILE- 164	3.9	0	Hydrophobic	false
C5D	CB	PRO- 166	4.03	0	Hydrophobic	false
C5N	CG	PRO- 166	4.28	0	Hydrophobic	false
C5D	CE2	PHE- 167	4.02	0	Hydrophobic	false
O2B	NZ	LYS- 191	2.68	146.01	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 191	3.33	0	Ionic (Protein Cationic)	false
C3B	CB	SER- 193	4.39	0	Hydrophobic	false
O2X	OG	SER- 193	2.63	151.24	H-Bond (Protein Donor)	false
O2X	N	ILE- 194	3.33	133.08	H-Bond (Protein Donor)	false
O3X	N	ILE- 194	2.98	159.52	H-Bond (Protein Donor)	false
O1X	N	GLY- 224	3.09	124.29	H-Bond (Protein Donor)	false
O3X	N	GLY- 224	2.94	145.58	H-Bond (Protein Donor)	false
N6A	OE2	GLU- 228	2.92	158.07	H-Bond (Ligand Donor)	false
C5B	CE2	PHE- 241	3.87	0	Hydrophobic	false
C4N	CG2	THR- 242	3.24	0	Hydrophobic	false
O1A	OG	SER- 244	2.6	149.91	H-Bond (Protein Donor)	false
C5B	CG1	VAL- 247	4.04	0	Hydrophobic	false
C3N	CB	GLU- 263	4.22	0	Hydrophobic	false
N7N	OE1	GLU- 263	2.94	140.98	H-Bond (Ligand Donor)	false
O7N	N	GLY- 265	2.68	149.37	H-Bond (Protein Donor)	false
O2D	N	GLY- 266	3.31	158.83	H-Bond (Protein Donor)	false
C2D	CB	CYS- 297	4.15	0	Hydrophobic	false
C4N	CB	CYS- 297	3.31	0	Hydrophobic	false
O3D	OE1	GLU- 395	2.79	139.72	H-Bond (Ligand Donor)	false
O2D	OE1	GLU- 395	3	165.66	H-Bond (Ligand Donor)	false
C5D	CE2	PHE- 397	3.76	0	Hydrophobic	false
C2D	CE1	PHE- 397	3.52	0	Hydrophobic	false
O3D	O	HOH- 637	3.2	164.08	H-Bond (Protein Donor)	false