scPDB - 4kp7 entry

Protein Data Bank Entry:

PDB ID : 4kp7

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-05-13

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:	28.599
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:	NAP
Metals:	MN3

Cavity properties

Ligandability	Volume (Å3)
0.559	553.500

% Hydrophobic	% Polar
40.85	59.15
According to VolSite

Ligand :

HET Code:	1UQ
Formula:	C10H12NO5PS
Molecular weight:	289.245 g/mol
DrugBank ID:	-
Buried Surface Area:	75.4 %
Polar Surface area:	138.84 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
25.9501	-4.90372	19.0622

Binding mode :

What is Poseview ?

2D View
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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
O1	NZ	LYS- 205	3.2	121.34	H-Bond (Protein Donor)	false
O4	N	SER- 232	3.2	131.14	H-Bond (Protein Donor)	false
O10	OG	SER- 269	3.06	171.57	H-Bond (Protein Donor)	false
O12	OG	SER- 270	2.57	154.06	H-Bond (Protein Donor)	false
O10	N	SER- 270	2.89	155.7	H-Bond (Protein Donor)	false
C14	CB	SER- 270	4.07	0	Hydrophobic	false
C15	CG	LYS- 295	3.95	0	Hydrophobic	false
C14	CE	MET- 298	4.35	0	Hydrophobic	false
C6	SD	MET- 298	3.43	0	Hydrophobic	false
C6	CD1	ILE- 302	3.98	0	Hydrophobic	false
S7	CG1	ILE- 302	4.39	0	Hydrophobic	false
O12	OG	SER- 306	2.52	128.64	H-Bond (Protein Donor)	false
S7	CB	SER- 306	4.2	0	Hydrophobic	false
O11	ND2	ASN- 311	2.82	167.83	H-Bond (Protein Donor)	false
O1	ND2	ASN- 311	3.02	153.63	H-Bond (Protein Donor)	false
O11	NZ	LYS- 312	3.81	0	Ionic (Protein Cationic)	false
O10	NZ	LYS- 312	3.04	0	Ionic (Protein Cationic)	false
O10	NZ	LYS- 312	3.04	137.05	H-Bond (Protein Donor)	false
C19	SG	CYS- 338	3.81	0	Hydrophobic	false
O4	MN	MN3- 501	2.04	0	Metal Acceptor	false
O1	MN	MN3- 501	2.1	0	Metal Acceptor	false
C6	C4N	NAP- 502	4.23	0	Hydrophobic	false