scPDB - 5dib entry

Protein Data Bank Entry:

PDB ID : 5dib

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2015-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Betaine-aldehyde dehydrogenase
ID:	Q9L4P8_STAAU
AC:	Q9L4P8
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.592
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.348	455.625

% Hydrophobic	% Polar
42.96	57.04
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	67.17 %
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
-16.8263	6.52634	25.4799

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
C1B	CG2	ILE- 153	3.91	0	Hydrophobic	false
C4B	CG2	ILE- 153	4	0	Hydrophobic	false
O3B	O	THR- 154	2.9	175.8	H-Bond (Ligand Donor)	false
C4N	CB	PRO- 155	3.65	0	Hydrophobic	false
O2N	NE1	TRP- 156	2.78	146.13	H-Bond (Protein Donor)	false
C5D	CZ2	TRP- 156	4.44	0	Hydrophobic	false
O2B	NZ	LYS- 180	2.64	171.21	H-Bond (Protein Donor)	false
C3B	CB	SER- 182	4.3	0	Hydrophobic	false
N6A	OD1	ASP- 218	3.49	158.6	H-Bond (Ligand Donor)	false
C4B	CE1	PHE- 231	4.04	0	Hydrophobic	false
C1B	CE1	PHE- 231	4.48	0	Hydrophobic	false
N7N	O	GLY- 233	2.96	133.27	H-Bond (Ligand Donor)	false
O2A	N	GLY- 234	2.6	147.43	H-Bond (Protein Donor)	false
O1A	OG1	THR- 237	2.81	169.39	H-Bond (Protein Donor)	false
C1B	CG2	THR- 237	4.47	0	Hydrophobic	false
O2D	OE1	GLU- 390	2.65	152.73	H-Bond (Ligand Donor)	false
C3D	CB	PHE- 392	4.27	0	Hydrophobic	false
C2D	CG	PHE- 392	3.61	0	Hydrophobic	false