scPDB - 4u3j entry

Protein Data Bank Entry:

PDB ID : 4u3j

Resolution :2.810 Å

Experimental Method : X-ray

Deposition Date : 2014-07-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tubulin beta chain
ID:	TBB_YEAST
AC:	P02557
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.636
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.052	401.625

% Hydrophobic	% Polar
30.25	69.75
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	70.48 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-62.0154	-66.8162	41.8755

Binding mode :

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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
O2B	N	GLN- 11	3.06	142.13	H-Bond (Protein Donor)	false
O1A	N	CYS- 12	2.85	139.99	H-Bond (Protein Donor)	false
C1'	CB	CYS- 12	4.12	0	Hydrophobic	false
O5'	OG	SER- 138	3.48	159.12	H-Bond (Protein Donor)	false
C1'	CB	SER- 138	4.1	0	Hydrophobic	false
C4'	CB	SER- 138	3.92	0	Hydrophobic	false
O3B	N	GLY- 142	3.19	172.15	H-Bond (Protein Donor)	false
O1G	OG1	THR- 143	2.73	143.08	H-Bond (Protein Donor)	false
O3B	N	THR- 143	3.35	173.99	H-Bond (Protein Donor)	false
O1B	N	GLY- 144	3.39	149.1	H-Bond (Protein Donor)	false
N2	OD1	ASN- 204	2.77	130.24	H-Bond (Ligand Donor)	false
C2'	CZ	TYR- 222	4.32	0	Hydrophobic	false
O6	ND2	ASN- 226	3.09	144.41	H-Bond (Protein Donor)	false
N1	OD1	ASN- 226	2.73	141.43	H-Bond (Ligand Donor)	false
O2G	MG	MG- 501	2.5	0	Metal Acceptor	false
O3G	MG	MG- 501	2	0	Metal Acceptor	false