scPDB - 4x4l entry

Protein Data Bank Entry:

PDB ID : 4x4l

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2014-12-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Retinal dehydrogenase 1
ID:	AL1A1_HUMAN
AC:	P00352
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.2.1.36

Chains:

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

Ligand binding site composition:

B-Factor:	44.935
Number of residues:	53
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:	CL CL CL

Cavity properties

Ligandability	Volume (Å3)
0.504	708.750

% Hydrophobic	% Polar
47.14	52.86
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	71.66 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-14.3953	44.7793	10.7636

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
C1B	CG2	ILE- 166	3.75	0	Hydrophobic	false
C4B	CG2	ILE- 166	3.9	0	Hydrophobic	false
O3B	O	ILE- 167	2.9	172.14	H-Bond (Ligand Donor)	false
C5B	CB	PRO- 168	4.28	0	Hydrophobic	false
C4N	CB	PRO- 168	3.51	0	Hydrophobic	false
O2N	NE1	TRP- 169	2.87	151.87	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 170	3.15	153.17	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 193	2.75	150.51	H-Bond (Protein Donor)	false
C3B	CB	ALA- 195	4.25	0	Hydrophobic	false
O2B	OE1	GLU- 196	2.56	152.51	H-Bond (Ligand Donor)	false
C1B	CE1	PHE- 244	4.4	0	Hydrophobic	false
C4B	CE1	PHE- 244	3.88	0	Hydrophobic	false
N7N	O	GLY- 246	3.37	156.55	H-Bond (Ligand Donor)	false
O1A	N	SER- 247	2.68	163.26	H-Bond (Protein Donor)	false
O1A	OG	SER- 247	2.78	150.19	H-Bond (Protein Donor)	false
C1D	CB	SER- 247	3.95	0	Hydrophobic	false
C4D	CB	SER- 247	3.82	0	Hydrophobic	false
N7N	OE2	GLU- 269	3.05	160.05	H-Bond (Ligand Donor)	false
O3D	NE2	GLN- 350	2.81	143.49	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 353	2.87	161.47	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 353	3.15	121.49	H-Bond (Protein Donor)	false
O2D	OE1	GLU- 400	2.52	167.54	H-Bond (Ligand Donor)	false
C3D	CD2	PHE- 402	4.2	0	Hydrophobic	false
C2D	CG	PHE- 402	3.65	0	Hydrophobic	false
C4N	CZ	PHE- 402	3.81	0	Hydrophobic	false