scPDB - 1dxy entry

Protein Data Bank Entry:

PDB ID : 1dxy

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 1996-08-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-2-hydroxyisocaproate dehydrogenase
ID:	DHD2_LACPA
AC:	P17584
Organism:	Lactobacillus paracasei
Reign:	Bacteria
TaxID:	1597
EC Number:	1.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	24.938
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.738	938.250

% Hydrophobic	% Polar
39.93	60.07
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	62.85 %
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
83.7106	44.968	-10.8388

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
C3N	CG1	ILE- 105	4.16	0	Hydrophobic	false
C4N	CD1	ILE- 105	3.8	0	Hydrophobic	false
O2A	N	HIS- 155	2.98	166.11	H-Bond (Protein Donor)	false
O1N	N	ILE- 156	2.96	148.36	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 156	3.91	0	Hydrophobic	false
O3B	OD2	ASP- 175	2.85	176.11	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 175	2.65	160.95	H-Bond (Ligand Donor)	false
C1B	CG	PRO- 176	4.46	0	Hydrophobic	false
C5D	CB	HIS- 204	4.33	0	Hydrophobic	false
O3D	O	VAL- 205	3.01	169.58	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 211	3.02	157.96	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 211	2.76	130.84	H-Bond (Ligand Donor)	false
N7N	O	THR- 232	2.77	134.29	H-Bond (Ligand Donor)	false
C4D	CB	ALA- 233	3.92	0	Hydrophobic	false
N7N	OD2	ASP- 258	3.29	159.79	H-Bond (Ligand Donor)	false
O7N	N	TYR- 298	3.41	124.49	H-Bond (Protein Donor)	false
C4N	CB	TYR- 298	4.25	0	Hydrophobic	false
O1N	O	HOH- 502	2.78	163.49	H-Bond (Protein Donor)	false
O2D	O	HOH- 603	3.4	134.98	H-Bond (Ligand Donor)	false