scPDB - 2e37 entry

Protein Data Bank Entry:

PDB ID : 2e37

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-11-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-lactate dehydrogenase
ID:	LDH_THET8
AC:	Q5SJA1
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	97 %
G	3 %

Ligand binding site composition:

B-Factor:	42.551
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.274	310.500

% Hydrophobic	% Polar
35.87	64.13
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	54 %
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
140.818	68.4929	122.835

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	MET- 10	3.2	155.9	H-Bond (Protein Donor)	false
O1N	N	VAL- 11	2.64	157.18	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 11	4.32	0	Hydrophobic	false
O2B	OD1	ASP- 32	2.91	169.14	H-Bond (Ligand Donor)	false
N3A	N	LEU- 33	3.23	161.04	H-Bond (Protein Donor)	false
C3B	CD2	LEU- 37	4.37	0	Hydrophobic	false
O4B	N	GLY- 76	3.29	132.95	H-Bond (Protein Donor)	false
O2D	O	VAL- 77	3.41	162.75	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 92	3.32	133.26	H-Bond (Protein Donor)	false
C4D	CG2	THR- 116	4.17	0	Hydrophobic	false
O7N	N	THR- 227	2.75	155.04	H-Bond (Protein Donor)	false
N7N	O	THR- 227	2.65	164.16	H-Bond (Ligand Donor)	false
O1N	O	HOH- 1410	2.53	179.95	H-Bond (Protein Donor)	false