scPDB - 4gqb entry

Protein Data Bank Entry:

PDB ID : 4gqb

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2012-08-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein arginine N-methyltransferase 5
ID:	ANM5_HUMAN
AC:	O14744
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
C	3 %

Ligand binding site composition:

B-Factor:	47.739
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.840	307.125

% Hydrophobic	% Polar
58.24	41.76
According to VolSite

Ligand :

HET Code:	0XU
Formula:	C15H22N7O5
Molecular weight:	380.379 g/mol
DrugBank ID:	-
Buried Surface Area:	81.97 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-32.6754	-37.5087	-4.75748

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
C2'	CB	PRO- 314	3.91	0	Hydrophobic	false
C3'	CD1	LEU- 319	4.38	0	Hydrophobic	false
CB	CE1	TYR- 324	4.2	0	Hydrophobic	false
C3'	CE1	TYR- 324	4.03	0	Hydrophobic	false
O3'	OH	TYR- 324	2.74	149.23	H-Bond (Protein Donor)	false
O2'	OH	TYR- 324	3.46	135.53	H-Bond (Protein Donor)	false
CB	CD2	PHE- 327	3.88	0	Hydrophobic	false
CG	CE2	PHE- 327	3.86	0	Hydrophobic	false
O	NZ	LYS- 333	3.05	0	Ionic (Protein Cationic)	false
O	OH	TYR- 334	3.12	145.55	H-Bond (Protein Donor)	false
OXT	OH	TYR- 334	2.71	145.74	H-Bond (Protein Donor)	false
N	O	GLY- 365	3.11	167.69	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 392	3.44	130.6	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 392	2.79	157.34	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 392	2.63	149.99	H-Bond (Ligand Donor)	false
N3	N	LYS- 393	3.39	148.5	H-Bond (Protein Donor)	false
N6	OD1	ASP- 419	2.83	145.98	H-Bond (Ligand Donor)	false
N1	N	MET- 420	2.98	170.18	H-Bond (Protein Donor)	false
NE	O	GLU- 435	2.82	144.32	H-Bond (Ligand Donor)	false
C1'	CD2	LEU- 436	4.37	0	Hydrophobic	false
NE	OE1	GLU- 444	3.63	0	Ionic (Ligand Cationic)	false
N	O	HOH- 832	3.01	150.29	H-Bond (Ligand Donor)	false
O2'	O	HOH- 947	2.73	135.07	H-Bond (Protein Donor)	false