scPDB - 4z61 entry

Protein Data Bank Entry:

PDB ID : 4z61

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2015-04-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phytosulfokine receptor 1
ID:	PSKR1_DAUCA
AC:	Q8LPB4
Organism:	Daucus carota
Reign:	Eukaryota
TaxID:	4039
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	15.316
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.929	830.250

% Hydrophobic	% Polar
48.37	51.63
According to VolSite

Ligand :

HET Code:	ILE_THR_GLN_TYS_TYS
Formula:	C33H44N6O16S2
Molecular weight:	844.863 g/mol
DrugBank ID:	-
Buried Surface Area:	64.14 %
Polar Surface area:	397.11 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	7
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	23

Mass center Coordinates

X	Y	Z
-114.217	23.0045	26.7921

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
O	NE	ARG- 310	2.8	154.46	H-Bond (Protein Donor)	false
O	NH1	ARG- 310	3.15	134.42	H-Bond (Protein Donor)	false
OXT	NE	ARG- 310	3.18	121.27	H-Bond (Protein Donor)	false
O	CZ	ARG- 310	3.4	0	Ionic (Protein Cationic)	false
O	OG	SER- 335	2.69	148.74	H-Bond (Protein Donor)	false
OG1	OD1	ASN- 356	2.76	128.98	H-Bond (Ligand Donor)	false
OXT	ND2	ASN- 356	2.93	141.09	H-Bond (Protein Donor)	false
CB	CD	LYS- 359	4.49	0	Hydrophobic	false
OG1	OG	SER- 380	2.88	148.91	H-Bond (Protein Donor)	false
CG2	CB	SER- 380	4.05	0	Hydrophobic	false
O	OG	SER- 382	3.49	169.18	H-Bond (Protein Donor)	false
CG2	CG1	VAL- 406	3.97	0	Hydrophobic	false
CB	CG2	THR- 408	4.15	0	Hydrophobic	false
CD1	CG2	THR- 408	3.96	0	Hydrophobic	false
O	OG1	THR- 408	2.77	166.25	H-Bond (Protein Donor)	false
CE1	CD1	LEU- 409	4.15	0	Hydrophobic	false
CG2	CD1	ILE- 431	3.71	0	Hydrophobic	false
CB	CB	ALA- 433	3.61	0	Hydrophobic	false
O3	OG	SER- 434	3.04	149.15	H-Bond (Protein Donor)	false
CE2	CB	SER- 434	4.17	0	Hydrophobic	false
CD1	CD2	LEU- 453	3.93	0	Hydrophobic	false
N	OD2	ASP- 455	2.85	152.66	H-Bond (Ligand Donor)	false
CD1	CE1	TYR- 477	4.15	0	Hydrophobic	false
CG2	CB	PHE- 515	3.8	0	Hydrophobic	false
CG2	CD1	PHE- 515	4.19	0	Hydrophobic	false
N	O	PHE- 516	2.96	176.08	H-Bond (Ligand Donor)	false
O	N	PHE- 516	2.76	165.54	H-Bond (Protein Donor)	false
CG	CE1	PHE- 516	3.7	0	Hydrophobic	false
CE1	CB	PHE- 516	3.38	0	Hydrophobic	false
CG1	CG	LYS- 517	4.34	0	Hydrophobic	false
CE2	CG	LYS- 518	3.6	0	Hydrophobic	false
CZ	CD	LYS- 518	3.48	0	Hydrophobic	false
CE2	CD	LYS- 518	3.95	0	Hydrophobic	false
CG	CB	LYS- 518	4.12	0	Hydrophobic	false
O1	NZ	LYS- 518	3.87	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 518	3.74	0	Ionic (Protein Cationic)	false
O3	NZ	LYS- 518	3.68	0	Ionic (Protein Cationic)	false
O	N	LYS- 518	3.15	147.72	H-Bond (Protein Donor)	false
O1	N	GLY- 525	3.3	127.91	H-Bond (Protein Donor)	false
CG1	CE1	PHE- 534	3.97	0	Hydrophobic	false
CD1	CZ	PHE- 534	3.75	0	Hydrophobic	false