scPDB - 5bmv entry

Protein Data Bank Entry:

PDB ID : 5bmv

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-05-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tubulin alpha-1B chain	Tubulin beta chain
ID:	TBA1B_BOVIN	TBB_PIG
AC:	P81947	P02554
Organism:	Bos taurus	Sus scrofa
Reign:	Eukaryota
TaxID:	9913	9823
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	54 %
B	46 %

Ligand binding site composition:

B-Factor:	37.952
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	GDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.331	1312.875

% Hydrophobic	% Polar
36.50	63.50
According to VolSite

Ligand :

HET Code:	VLB
Formula:	C46H60N4O9
Molecular weight:	812.990 g/mol
DrugBank ID:	DB00570
Buried Surface Area:	59.27 %
Polar Surface area:	156.49 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	5
Rings:	9
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-0.935932	35.4233	18.0318

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
C22	CB	LYS- 176	4	0	Hydrophobic	false
C53	CG1	VAL- 177	4.47	0	Hydrophobic	false
C70	CG1	VAL- 177	4.04	0	Hydrophobic	false
N9	OD1	ASP- 179	3.88	0	Ionic (Ligand Cationic)	false
C22	CZ	TYR- 210	3.8	0	Hydrophobic	false
C33	CE1	TYR- 210	3.9	0	Hydrophobic	false
C33	CE1	PHE- 214	3.67	0	Hydrophobic	false
O72	O	PRO- 222	2.74	151.65	H-Bond (Ligand Donor)	false
C33	CG	PRO- 222	4.12	0	Hydrophobic	false
C71	CD1	TYR- 224	4.3	0	Hydrophobic	false
C70	CZ	TYR- 224	3.71	0	Hydrophobic	false
C71	CD2	LEU- 227	3.57	0	Hydrophobic	false
C58	CD2	LEU- 248	4.25	0	Hydrophobic	false
C61	CD1	LEU- 248	4.01	0	Hydrophobic	false
C76	CB	PRO- 325	3.84	0	Hydrophobic	false
C65	CB	PRO- 325	3.51	0	Hydrophobic	false
C61	CG	PRO- 325	4	0	Hydrophobic	false
C64	CB	PRO- 325	3.89	0	Hydrophobic	false
C63	CG2	VAL- 328	4.2	0	Hydrophobic	false
C64	CB	VAL- 328	3.94	0	Hydrophobic	false
C21	CG1	VAL- 328	4.41	0	Hydrophobic	false
N66	OD1	ASN- 329	2.98	155.73	H-Bond (Ligand Donor)	false
C20	CB	ASN- 329	4.47	0	Hydrophobic	false
C30	CB	ASN- 329	3.39	0	Hydrophobic	false
C6	CD1	ILE- 332	4.34	0	Hydrophobic	false
C21	CD1	ILE- 332	3.83	0	Hydrophobic	false
C7	CB	PHE- 351	3.69	0	Hydrophobic	false
C7	CG2	VAL- 353	4.33	0	Hydrophobic	false
C21	CG2	VAL- 353	4.02	0	Hydrophobic	false
C63	CG1	VAL- 353	3.3	0	Hydrophobic	false
C62	CD1	ILE- 355	3.7	0	Hydrophobic	false