scPDB - 2pla entry

Protein Data Bank Entry:

PDB ID : 2pla

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2007-04-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycerol-3-phosphate dehydrogenase 1-like protein
ID:	GPD1L_HUMAN
AC:	Q8N335
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.579
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.230	708.750

% Hydrophobic	% Polar
48.57	51.43
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.93 %
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
69.2292	-74.9787	-1.0077

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
O2A	N	ASN- 15	3.1	144.46	H-Bond (Protein Donor)	false
N7N	OD1	ASN- 15	3.16	165.02	H-Bond (Ligand Donor)	false
O1N	N	TRP- 16	3	168.95	H-Bond (Protein Donor)	false
O2N	N	TRP- 16	3.18	122.09	H-Bond (Protein Donor)	false
C5D	CB	TRP- 16	4.28	0	Hydrophobic	false
C3N	CB	TRP- 16	3.64	0	Hydrophobic	false
O2N	N	GLY- 17	3.12	146.42	H-Bond (Protein Donor)	false
C2B	CD1	PHE- 43	4.46	0	Hydrophobic	false
DuAr	DuAr	PHE- 43	3.66	0	Aromatic Face/Face	false
C3B	CZ	TYR- 65	3.63	0	Hydrophobic	false
C5B	CE2	TYR- 65	4.01	0	Hydrophobic	false
C5D	CG2	VAL- 94	3.65	0	Hydrophobic	false
C5B	CG	PRO- 96	4.02	0	Hydrophobic	false
C1B	CE2	PHE- 99	4.22	0	Hydrophobic	false
DuAr	DuAr	PHE- 99	3.48	0	Aromatic Face/Face	false
O3D	N	LYS- 122	2.99	170.94	H-Bond (Protein Donor)	false
C5N	CB	ASN- 153	4.34	0	Hydrophobic	false
O7N	N	ALA- 155	3.03	171.82	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 271	3.16	123.96	H-Bond (Protein Donor)	false
O1A	N	LYS- 298	2.69	142.63	H-Bond (Protein Donor)	false
O3D	OE1	GLN- 300	2.83	144.27	H-Bond (Ligand Donor)	false
O7N	O	HOH- 621	3.47	142.02	H-Bond (Protein Donor)	false