scPDB - 2rcy entry

Protein Data Bank Entry:

PDB ID : 2rcy

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-09-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyrroline-5-carboxylate reductase
ID:	Q8IDC6_PLAF7
AC:	Q8IDC6
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	19 %
B	2 %
E	79 %

Ligand binding site composition:

B-Factor:	42.533
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.150	1069.875

% Hydrophobic	% Polar
45.11	54.89
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	61.03 %
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
51.3115	13.83	-24.6218

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
O1A	N	GLN- 14	3.24	178.08	H-Bond (Protein Donor)	false
O2N	N	MET- 15	2.93	176.48	H-Bond (Protein Donor)	false
C5D	CB	MET- 15	4.43	0	Hydrophobic	false
C3N	CG	MET- 15	3.54	0	Hydrophobic	false
C4N	SD	MET- 15	3.54	0	Hydrophobic	false
C2B	CG	PRO- 39	4.45	0	Hydrophobic	false
O3B	NZ	LYS- 42	3.48	128.97	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 42	3.92	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 42	2.81	0	Ionic (Protein Cationic)	false
N1A	ND2	ASN- 52	3.24	154.33	H-Bond (Protein Donor)	false
O3D	O	VAL- 66	2.67	162.75	H-Bond (Ligand Donor)	false
C5B	CG	LYS- 67	4.48	0	Hydrophobic	false
C3D	CG	PRO- 68	4.5	0	Hydrophobic	false
C4D	CD1	ILE- 90	4.46	0	Hydrophobic	false
O2D	N	GLY- 92	2.76	139.15	H-Bond (Protein Donor)	false
C5N	SD	MET- 113	3.46	0	Hydrophobic	false
N7N	O	ASN- 222	3.37	171.39	H-Bond (Ligand Donor)	false
O1N	OG	SER- 225	2.75	171.68	H-Bond (Protein Donor)	false
C2D	CB	SER- 225	4.34	0	Hydrophobic	false
N7N	OG	SER- 225	3.39	125.99	H-Bond (Ligand Donor)	false
O7N	O	HOH- 306	2.89	165.52	H-Bond (Protein Donor)	false
O2N	O	HOH- 308	3.01	169.46	H-Bond (Protein Donor)	false