scPDB - 5cb4 entry

Protein Data Bank Entry:

PDB ID : 5cb4

Resolution :2.190 Å

Experimental Method : X-ray

Deposition Date : 2015-06-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tubulin tyrosine ligase
ID:	E1BQ43_CHICK
AC:	E1BQ43
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	74.644
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.652	502.875

% Hydrophobic	% Polar
44.97	55.03
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	59.39 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
9.1011	-51.4203	-100.509

Binding mode :

What is Poseview ?

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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	NZ	LYS- 74	3.4	152.3	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 74	3.4	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 74	3.77	0	Ionic (Protein Cationic)	false
N6	OE1	GLN- 183	2.89	170.62	H-Bond (Ligand Donor)	false
N6	O	LYS- 184	2.82	146.57	H-Bond (Ligand Donor)	false
N1	N	LEU- 186	3.07	174.55	H-Bond (Protein Donor)	false
N3	NZ	LYS- 198	3.28	167.9	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 202	3.76	0	Ionic (Protein Cationic)	false
O3G	NH2	ARG- 202	2.51	121.96	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 222	3.47	161.33	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 240	4.1	0	Hydrophobic	false
C1'	CD2	LEU- 240	4.23	0	Hydrophobic	false
O3'	OG1	THR- 241	3.25	152.01	H-Bond (Ligand Donor)	false
O2'	N	THR- 241	3.47	146.16	H-Bond (Protein Donor)	false
O3G	OD2	ASP- 318	2.7	161.3	H-Bond (Protein Donor)	false