scPDB - 4yr9 entry

Protein Data Bank Entry:

PDB ID : 4yr9

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2015-03-14

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, mitochondrial
ID:	TDH_MOUSE
AC:	Q8K3F7
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.1.1.103

Chains:

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

Ligand binding site composition:

B-Factor:	31.582
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.449	1181.250

% Hydrophobic	% Polar
49.14	50.86
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	72.29 %
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
-16.2404	-28.4827	100.41

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
O1A	N	GLN- 66	3.14	162.56	H-Bond (Protein Donor)	false
O2N	N	LEU- 67	3.02	152.84	H-Bond (Protein Donor)	false
C3N	CD1	LEU- 67	4.35	0	Hydrophobic	false
C5D	CD1	LEU- 67	3.77	0	Hydrophobic	false
O3B	OD2	ASP- 88	2.75	161.99	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 88	3.47	138.99	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 88	2.79	167.44	H-Bond (Ligand Donor)	false
O3B	NH2	ARG- 90	2.67	144.6	H-Bond (Protein Donor)	false
O3B	NE	ARG- 90	3.21	127.88	H-Bond (Protein Donor)	false
O2B	NE	ARG- 90	3.01	144.44	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 106	2.7	130.11	H-Bond (Ligand Donor)	false
N1A	N	ILE- 107	2.77	171.74	H-Bond (Protein Donor)	false
C5D	CG	TYR- 128	3.69	0	Hydrophobic	false
C4D	CD1	TYR- 128	3.99	0	Hydrophobic	false
C1B	CB	SER- 129	4.25	0	Hydrophobic	false
C3D	CB	ALA- 130	4	0	Hydrophobic	false
C2D	CD2	LEU- 132	3.79	0	Hydrophobic	false
C4D	CG	PRO- 168	3.76	0	Hydrophobic	false
C5N	CB	THR- 170	3.69	0	Hydrophobic	false
C2D	CE1	TYR- 195	4.42	0	Hydrophobic	false
O2D	OH	TYR- 195	2.72	165.28	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 199	3.16	172.65	H-Bond (Protein Donor)	false
C5N	CB	TYR- 222	3.52	0	Hydrophobic	false
C3N	CD1	ILE- 225	3.83	0	Hydrophobic	false
O2N	O	HOH- 1109	2.76	155.11	H-Bond (Protein Donor)	false