scPDB - 2y42 entry

Protein Data Bank Entry:

PDB ID : 2y42

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-01-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-isopropylmalate dehydrogenase
ID:	LEU3_THET8
AC:	Q5SIY4
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	1.1.1.85

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	42.206
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.243	715.500

% Hydrophobic	% Polar
37.26	62.74
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	48.94 %
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
-6.75568	-1.0828	-7.96705

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
O7N	N	VAL- 72	3.38	176.83	H-Bond (Protein Donor)	false
O3D	OD2	ASP- 78	2.78	157.49	H-Bond (Ligand Donor)	false
O3D	OD1	ASP- 78	2.92	134.4	H-Bond (Ligand Donor)	false
N6A	NE2	HIS- 273	3.31	147.19	H-Bond (Ligand Donor)	false
O1A	N	GLY- 274	2.78	164.28	H-Bond (Protein Donor)	false
O4D	OG	SER- 275	3.31	160.81	H-Bond (Protein Donor)	false
O4D	N	SER- 275	3.17	168.09	H-Bond (Protein Donor)	false
O2A	N	ALA- 276	2.8	143.48	H-Bond (Protein Donor)	false
C2B	CB	ALA- 276	3.66	0	Hydrophobic	false
O3B	OD2	ASP- 278	2.73	150.83	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 278	2.77	163.16	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 278	2.64	125.06	H-Bond (Ligand Donor)	false
N6A	O	ASN- 286	3.05	166.86	H-Bond (Ligand Donor)	false
N1A	N	ASN- 286	2.94	158.23	H-Bond (Protein Donor)	false
N7N	O	HOH- 2044	2.9	133.49	H-Bond (Ligand Donor)	false