scPDB - 2czc entry

Protein Data Bank Entry:

PDB ID : 2czc

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-07-13

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_PYRHO
AC:	O59494
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	1.2.1.59

Chains:

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

Ligand binding site composition:

B-Factor:	30.244
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.754	286.875

% Hydrophobic	% Polar
62.35	37.65
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	52.73 %
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
12.4157	-22.6665	-26.1681

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	THR- 12	2.91	175.39	H-Bond (Protein Donor)	false
O1A	OG1	THR- 12	3.28	148.65	H-Bond (Protein Donor)	false
O1N	N	ILE- 13	2.98	177.82	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 13	3.58	0	Hydrophobic	false
C1B	CG2	THR- 35	4.46	0	Hydrophobic	false
C5B	CG	PRO- 88	4.06	0	Hydrophobic	false
C4D	CB	GLN- 109	3.84	0	Hydrophobic	false
O3D	N	GLY- 111	3.29	126.44	H-Bond (Protein Donor)	false
C4N	SG	CYS- 141	3.59	0	Hydrophobic	false
O7N	NH1	ARG- 167	3.38	127.22	H-Bond (Protein Donor)	false
N7N	OD1	ASP- 170	3.02	149.23	H-Bond (Ligand Donor)	false
O1N	O	HOH- 610	2.65	180	H-Bond (Protein Donor)	false
O3D	O	HOH- 642	2.68	163.38	H-Bond (Ligand Donor)	false
N1A	O	HOH- 675	2.99	165.73	H-Bond (Protein Donor)	false