scPDB - 1bi9 entry

Protein Data Bank Entry:

PDB ID : 1bi9

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1998-06-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Retinal dehydrogenase 2
ID:	AL1A2_RAT
AC:	Q63639
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.201
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.561	394.875

% Hydrophobic	% Polar
58.97	41.03
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	58.39 %
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
-14.6433	74.4753	21.5002

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- 165	3.61	0	Hydrophobic	false
C5B	CB	PRO- 167	4.37	0	Hydrophobic	false
O1N	NE1	TRP- 168	3.21	144.69	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 192	2.56	150.74	H-Bond (Protein Donor)	false
C3B	CB	ALA- 194	4.5	0	Hydrophobic	false
O2B	OE2	GLU- 195	3.39	159.75	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 195	3.17	145.06	H-Bond (Ligand Donor)	false
C1B	CE2	PHE- 243	4.34	0	Hydrophobic	false
C4B	CE2	PHE- 243	3.89	0	Hydrophobic	false
O1A	N	SER- 246	2.77	161.96	H-Bond (Protein Donor)	false
O1A	OG	SER- 246	2.62	161.7	H-Bond (Protein Donor)	false