scPDB - 2d8a entry

Protein Data Bank Entry:

PDB ID : 2d8a

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2005-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-threonine 3-dehydrogenase
ID:	TDH_PYRHO
AC:	O58389
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.734
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.665	756.000

% Hydrophobic	% Polar
41.07	58.93
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	51.71 %
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
20.3344	36.7539	15.9796

Binding mode :

What is Poseview ?

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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
O2N	N	LEU- 179	3.27	156.94	H-Bond (Protein Donor)	false
C5N	CD1	LEU- 179	3.79	0	Hydrophobic	false
C5D	CD1	LEU- 179	4.03	0	Hydrophobic	false
O3B	OE1	GLU- 199	2.9	143.19	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 199	2.78	161.28	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 204	3.43	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 204	2.55	120.36	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 204	2.76	165.1	H-Bond (Protein Donor)	false
C1B	CB	SER- 244	4.1	0	Hydrophobic	false
N7N	O	LEU- 266	3.16	152.54	H-Bond (Ligand Donor)	false
C3N	CD1	LEU- 266	3.75	0	Hydrophobic	false
O3D	N	LEU- 268	2.72	163.25	H-Bond (Protein Donor)	false
C3N	CD1	LEU- 268	4.45	0	Hydrophobic	false
N7N	O	ILE- 291	2.91	122.83	H-Bond (Ligand Donor)	false
O7N	OG1	THR- 292	2.64	166.45	H-Bond (Protein Donor)	false
O2N	O	HOH- 592	2.71	179.96	H-Bond (Protein Donor)	false
O7N	O	HOH- 763	3.39	179.97	H-Bond (Protein Donor)	false