scPDB - 3cb2 entry

Protein Data Bank Entry:

PDB ID : 3cb2

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tubulin gamma-1 chain
ID:	TBG1_HUMAN
AC:	P23258
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.686
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.439	631.125

% Hydrophobic	% Polar
32.09	67.91
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	66.94 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
17.8336	17.2183	15.2385

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	N	GLN- 12	2.86	174.76	H-Bond (Protein Donor)	false
N7	NE2	GLN- 12	2.98	161.87	H-Bond (Protein Donor)	false
O1A	N	CYS- 13	2.77	164.47	H-Bond (Protein Donor)	false
C1'	CB	CYS- 13	4.32	0	Hydrophobic	false
O6	NE2	GLN- 16	2.64	144.78	H-Bond (Protein Donor)	false
O5'	OG	SER- 140	2.84	146.29	H-Bond (Protein Donor)	false
O4'	OG	SER- 140	3.2	137.81	H-Bond (Protein Donor)	false
C4'	CB	SER- 140	3.79	0	Hydrophobic	false
C1'	CB	SER- 140	4.37	0	Hydrophobic	false
C4'	CB	ALA- 142	4.24	0	Hydrophobic	false
O3B	N	GLY- 144	2.83	149.04	H-Bond (Protein Donor)	false
O1B	N	THR- 145	3.48	120.19	H-Bond (Protein Donor)	false
O3B	N	THR- 145	2.78	176.51	H-Bond (Protein Donor)	false
O1B	N	GLY- 146	2.76	167.9	H-Bond (Protein Donor)	false
N2	OD1	ASN- 207	2.96	151.77	H-Bond (Ligand Donor)	false
N3	ND2	ASN- 207	3.2	174.17	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 225	4.1	0	Hydrophobic	false
C1'	CE2	PHE- 225	4.3	0	Hydrophobic	false
DuAr	DuAr	PHE- 225	3.92	0	Aromatic Face/Face	false
O6	ND2	ASN- 229	2.89	172.03	H-Bond (Protein Donor)	false
N1	OD1	ASN- 229	2.68	170	H-Bond (Ligand Donor)	false
N2	OD1	ASN- 229	3.42	127.98	H-Bond (Ligand Donor)	false
O1B	O	HOH- 504	3.1	179.97	H-Bond (Protein Donor)	false
O1B	O	HOH- 505	2.74	179.97	H-Bond (Protein Donor)	false
O3'	O	HOH- 507	3.04	179.96	H-Bond (Protein Donor)	false
O3'	O	HOH- 532	2.89	179.98	H-Bond (Protein Donor)	false