scPDB - 4dl9 entry

Protein Data Bank Entry:

PDB ID : 4dl9

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2012-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-(hydroxymethyl)glutathione dehydrogenase
ID:	D2Y3F4_SOLLC
AC:	D2Y3F4
Organism:	Solanum lycopersicum
Reign:	Eukaryota
TaxID:	4081
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	26.281
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.628	1893.375

% Hydrophobic	% Polar
52.76	47.24
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	57.53 %
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
-27.5262	8.43966	-2.99293

Binding mode :

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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
C5N	SG	CYS- 177	3.51	0	Hydrophobic	false
C3N	CG2	THR- 181	3.47	0	Hydrophobic	false
O2N	N	VAL- 206	2.84	165.88	H-Bond (Protein Donor)	false
C5D	CB	VAL- 206	3.86	0	Hydrophobic	false
C4D	CG2	VAL- 206	4.32	0	Hydrophobic	false
O3B	OD2	ASP- 226	2.65	159.98	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 226	3.5	130.94	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 226	2.61	162.07	H-Bond (Ligand Donor)	false
C3B	CE	LYS- 231	4.28	0	Hydrophobic	false
O3B	NZ	LYS- 231	3.33	142.28	H-Bond (Protein Donor)	false
C1B	CG1	ILE- 272	4.14	0	Hydrophobic	false
N7N	O	VAL- 295	2.87	164.28	H-Bond (Ligand Donor)	false
O3D	N	VAL- 297	3.27	150.71	H-Bond (Protein Donor)	false
O2D	N	VAL- 297	3.34	144.62	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 297	4.34	0	Hydrophobic	false
N7N	O	THR- 320	2.81	158.87	H-Bond (Ligand Donor)	false
O7N	N	PHE- 322	2.67	178.5	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 372	3.16	162.41	H-Bond (Protein Donor)	false
O2N	O	HOH- 504	2.86	176.56	H-Bond (Protein Donor)	false
O3D	O	HOH- 689	2.63	148.8	H-Bond (Ligand Donor)	false