scPDB - 1zgd entry

Protein Data Bank Entry:

PDB ID : 1zgd

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2005-04-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chalcone reductase
ID:	Q40309_MEDSA
AC:	Q40309
Organism:	Medicago sativa
Reign:	Eukaryota
TaxID:	3879
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.355
Number of residues:	51
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.834	1036.125

% Hydrophobic	% Polar
48.86	51.14
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	67.23 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
40.0157	-21.6053	49.4297

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
O3D	N	SER- 27	3.15	136.23	H-Bond (Protein Donor)	false
C5D	CB	ALA- 28	3.22	0	Hydrophobic	false
C2D	CB	ALA- 28	3.67	0	Hydrophobic	false
O3B	OD2	ASP- 30	2.7	162.06	H-Bond (Ligand Donor)	false
O3D	OD1	ASP- 53	2.82	158.6	H-Bond (Ligand Donor)	false
O2D	OH	TYR- 58	2.6	166.26	H-Bond (Ligand Donor)	false
C2D	CE2	TYR- 58	3.42	0	Hydrophobic	false
N7N	OG	SER- 166	2.97	131.53	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 167	2.94	163.23	H-Bond (Protein Donor)	false
N7N	OE1	GLN- 188	3.2	150.01	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 214	3.8	0	Aromatic Face/Face	false
C3N	CB	PHE- 214	3.96	0	Hydrophobic	false
O1N	OG	SER- 215	2.94	155.15	H-Bond (Protein Donor)	false
O2N	N	SER- 215	2.71	134.2	H-Bond (Protein Donor)	false
O1A	N	VAL- 217	2.85	150.45	H-Bond (Protein Donor)	false
C5B	CG2	VAL- 217	4.08	0	Hydrophobic	false
O1A	N	LYS- 219	2.97	155.28	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 219	2.72	161.75	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 219	2.72	0	Ionic (Protein Cationic)	false
O2A	N	LYS- 263	2.95	164.94	H-Bond (Protein Donor)	false
C5B	CB	LYS- 263	4.42	0	Hydrophobic	false
C5D	CB	LYS- 263	3.88	0	Hydrophobic	false
O1X	CZ	ARG- 269	3.74	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 269	3.46	0	Ionic (Protein Cationic)	false
O3X	NE	ARG- 269	3.32	132.71	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 269	2.76	156.82	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 273	3.17	167.62	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 273	3.02	149.46	H-Bond (Ligand Donor)	false