scPDB - 2x06 entry

Protein Data Bank Entry:

PDB ID : 2x06

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-12-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-sulfolactate dehydrogenase
ID:	COMC_METJA
AC:	Q58820
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	11 %
H	89 %

Ligand binding site composition:

B-Factor:	35.079
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.900	421.875

% Hydrophobic	% Polar
54.40	45.60
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	59.38 %
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
16.7502	153.997	-8.51123

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
C3D	CE2	PHE- 41	4.15	0	Hydrophobic	false
C5D	CD2	PHE- 41	3.3	0	Hydrophobic	false
N7N	O	GLY- 118	3.02	131.97	H-Bond (Ligand Donor)	false
O2D	N	ALA- 120	3.05	162.85	H-Bond (Protein Donor)	false
C5N	CB	THR- 156	4.02	0	Hydrophobic	false
C2D	CB	PRO- 158	4.17	0	Hydrophobic	false
C5N	CB	PRO- 158	3.96	0	Hydrophobic	false
C4N	CG	PRO- 158	3.8	0	Hydrophobic	false
C4B	CD1	LEU- 172	4.32	0	Hydrophobic	false
O3B	N	ASP- 173	3.17	162.31	H-Bond (Protein Donor)	false
O2D	OD1	ASP- 173	2.81	164.49	H-Bond (Ligand Donor)	false
C5B	CB	MET- 174	3.72	0	Hydrophobic	false
O1N	N	ALA- 175	2.96	157.12	H-Bond (Protein Donor)	false
C5N	CB	ALA- 175	3.85	0	Hydrophobic	false
O1A	NZ	LYS- 225	3.37	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 225	2.7	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 225	2.7	154.08	H-Bond (Protein Donor)	false
O2B	N	GLY- 304	2.96	169.17	H-Bond (Protein Donor)	false
O2B	OE2	GLU- 307	3.45	130.39	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 307	2.78	161.64	H-Bond (Ligand Donor)	false
N1A	O	HOH- 2040	2.97	132.46	H-Bond (Protein Donor)	false
O2B	O	HOH- 2052	2.93	179.98	H-Bond (Protein Donor)	false