scPDB - 4ydq entry

Protein Data Bank Entry:

PDB ID : 4ydq

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-02-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proline--tRNA ligase
ID:	SYP_PLAF7
AC:	Q8I5R7
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	6.1.1.15

Chains:

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

Ligand binding site composition:

B-Factor:	40.990
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:	ANP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.717	637.875

% Hydrophobic	% Polar
56.08	43.92
According to VolSite

Ligand :

HET Code:	HFG
Formula:	C16H18BrClN3O3
Molecular weight:	415.689 g/mol
DrugBank ID:	DB04866
Buried Surface Area:	74.52 %
Polar Surface area:	86.58 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
196.327	-14.2644	19.293

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
CL1	CD1	LEU- 325	4.35	0	Hydrophobic	false
CL1	CB	PHE- 335	4.42	0	Hydrophobic	false
C7	CB	PHE- 335	4	0	Hydrophobic	false
BR1	CB	GLU- 338	3.76	0	Hydrophobic	false
BR1	CG2	VAL- 339	3.59	0	Hydrophobic	false
CL1	CG2	VAL- 339	4.42	0	Hydrophobic	false
BR1	CB	PRO- 358	3.7	0	Hydrophobic	false
CL1	CG	PRO- 358	3.5	0	Hydrophobic	false
C6	CG	PRO- 358	3.55	0	Hydrophobic	false
C7	CB	PRO- 358	3.51	0	Hydrophobic	false
C5	CG2	THR- 359	3.81	0	Hydrophobic	false
N1'	OE2	GLU- 361	2.68	165.42	H-Bond (Ligand Donor)	false
N1'	OE2	GLU- 361	2.68	0	Ionic (Ligand Cationic)	false
N1'	OE1	GLU- 361	3.6	0	Ionic (Ligand Cationic)	false
C8	CD	ARG- 390	4.07	0	Hydrophobic	false
C5'	CZ3	TRP- 407	3.54	0	Hydrophobic	false
C5'	CB	GLU- 409	3.93	0	Hydrophobic	false
C3'	CZ	PHE- 454	3.82	0	Hydrophobic	false
C1'	CD1	PHE- 454	3.63	0	Hydrophobic	false
O7'	OG1	THR- 478	3.03	155.05	H-Bond (Protein Donor)	false
O7'	NE2	HIS- 480	2.77	177.99	H-Bond (Protein Donor)	false
C39	C5'	ANP- 801	4.31	0	Hydrophobic	false
O7'	O1A	ANP- 801	2.71	165.96	H-Bond (Ligand Donor)	false