scPDB - 4gae entry

Protein Data Bank Entry:

PDB ID : 4gae

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-07-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
ID:	DXR_PLAFX
AC:	O96693
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	137071
EC Number:	1.1.1.267

Chains:

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

Ligand binding site composition:

B-Factor:	40.200
Number of residues:	50
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.708	354.375

% Hydrophobic	% Polar
58.10	41.90
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	72.26 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
0.683979	-23.8525	13.6286

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
O3B	OG1	THR- 86	3.05	159.1	H-Bond (Ligand Donor)	false
O3B	N	THR- 86	3.41	120.1	H-Bond (Protein Donor)	false
O1X	OG1	THR- 86	2.73	155.99	H-Bond (Protein Donor)	false
O2A	N	SER- 88	2.81	155.51	H-Bond (Protein Donor)	false
N7N	OG	SER- 88	2.8	141.8	H-Bond (Ligand Donor)	false
O2N	N	ILE- 89	2.88	165.44	H-Bond (Protein Donor)	false
C5D	CG1	ILE- 89	4.18	0	Hydrophobic	false
C3N	CD1	ILE- 89	3.54	0	Hydrophobic	false
C2B	CB	ASN- 115	4.35	0	Hydrophobic	false
O2B	N	ASN- 115	3.34	138.23	H-Bond (Protein Donor)	false
O2X	N	ASN- 115	2.93	140.75	H-Bond (Protein Donor)	false
O2X	N	LYS- 116	2.74	139.64	H-Bond (Protein Donor)	false
O1X	OG	SER- 117	2.85	178.5	H-Bond (Protein Donor)	false
O2X	N	SER- 117	2.84	174.46	H-Bond (Protein Donor)	false
C5B	CB	ASP- 182	4.21	0	Hydrophobic	false
C3D	CB	ASP- 182	3.95	0	Hydrophobic	false
O3D	ND2	ASN- 204	3.13	132.58	H-Bond (Protein Donor)	false
O3D	OE1	GLU- 206	2.98	140.96	H-Bond (Ligand Donor)	false
O1N	N	GLY- 299	2.89	157.65	H-Bond (Protein Donor)	false
C2D	CD1	ILE- 302	4.31	0	Hydrophobic	false
C3N	CD1	ILE- 302	3.97	0	Hydrophobic	false
C4N	CE	MET- 360	3.58	0	Hydrophobic	false
O2N	O	HOH- 1552	3.05	179.97	H-Bond (Protein Donor)	false