scPDB - 2yyy entry

Protein Data Bank Entry:

PDB ID : 2yyy

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2007-05-02

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:	G3P_METJA
AC:	Q58546
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	1.2.1.59

Chains:

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

Ligand binding site composition:

B-Factor:	18.384
Number of residues:	55
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.838	610.875

% Hydrophobic	% Polar
46.41	53.59
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	59.46 %
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
28.0452	-3.74806	15.9514

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
O1A	N	SER- 12	2.84	175.36	H-Bond (Protein Donor)	false
O1N	N	ILE- 13	3.07	176.58	H-Bond (Protein Donor)	false
C4N	CD1	ILE- 13	3.72	0	Hydrophobic	false
O2X	NZ	LYS- 34	3.22	151.68	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 34	2.75	129.12	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 34	3.22	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 34	2.75	0	Ionic (Protein Cationic)	false
O1X	OG1	THR- 35	2.84	147.79	H-Bond (Protein Donor)	false
O2X	N	THR- 35	2.73	142.54	H-Bond (Protein Donor)	false
O2X	N	LYS- 36	2.79	152.77	H-Bond (Protein Donor)	false
C5B	CG	PRO- 90	4.2	0	Hydrophobic	false
N1A	ND2	ASN- 97	3.33	160.59	H-Bond (Protein Donor)	false
C4D	CB	GLN- 112	3.51	0	Hydrophobic	false
O3D	N	GLY- 114	3.09	133.13	H-Bond (Protein Donor)	false
C4N	CB	CYS- 144	3.99	0	Hydrophobic	false
O7N	NH2	ARG- 172	3.49	125.73	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 175	2.84	172.98	H-Bond (Ligand Donor)	false
C5N	CG2	VAL- 311	4.06	0	Hydrophobic	false
O1N	O	HOH- 1004	2.72	179.96	H-Bond (Protein Donor)	false
O3D	O	HOH- 1005	2.65	166.16	H-Bond (Ligand Donor)	false
N1A	O	HOH- 1062	2.82	160.25	H-Bond (Protein Donor)	false