scPDB - 2g5c entry

Protein Data Bank Entry:

PDB ID : 2g5c

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-02-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prephenate dehydrogenase
ID:	O67636_AQUAE
AC:	O67636
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.879
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.174	1390.500

% Hydrophobic	% Polar
38.83	61.17
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.38 %
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
35.24	4.90139	37.9729

Binding mode :

What is Poseview ?

2D View
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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
O1A	N	PHE- 40	3.02	178.29	H-Bond (Protein Donor)	false
O1N	N	MET- 41	2.77	173.57	H-Bond (Protein Donor)	false
C5D	CG	MET- 41	4.21	0	Hydrophobic	false
C3N	SD	MET- 41	3.78	0	Hydrophobic	false
C5N	CE	MET- 41	3.6	0	Hydrophobic	false
O3B	OD2	ASP- 62	2.69	162.63	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 62	2.59	158.56	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 62	3.46	129.46	H-Bond (Ligand Donor)	false
O3B	OG	SER- 67	3.21	172.63	H-Bond (Protein Donor)	false
C1B	CB	SER- 99	4.4	0	Hydrophobic	false
C2D	CB	SER- 126	4.13	0	Hydrophobic	false
O2D	OG	SER- 126	3.17	151.12	H-Bond (Protein Donor)	false
O2D	N	SER- 126	3.04	157.56	H-Bond (Protein Donor)	false
O1A	N	GLY- 156	2.9	175.26	H-Bond (Protein Donor)	false
C3N	SD	MET- 258	4.26	0	Hydrophobic	false
C3D	SD	MET- 258	4.14	0	Hydrophobic	false
O1N	O	HOH- 5689	2.61	171.66	H-Bond (Protein Donor)	false