scPDB - 3vwd entry

Protein Data Bank Entry:

PDB ID : 3vwd

Resolution :1.250 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:	Alpha-tubulin N-acetyltransferase 1
ID:	ATAT_HUMAN
AC:	Q5SQI0
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:	7.838
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.968	745.875

% Hydrophobic	% Polar
55.20	44.80
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	67.4 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-14.7361	4.52769	-6.75039

Binding mode :

What is Poseview ?

2D View
3D View

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
C6P	CB	ALA- 57	4.15	0	Hydrophobic	false
C6P	CG	GLN- 58	4.19	0	Hydrophobic	false
C2P	CG	GLN- 58	4.09	0	Hydrophobic	false
CH3	CG2	ILE- 121	4.14	0	Hydrophobic	false
CEP	CD1	PHE- 124	3.7	0	Hydrophobic	false
N4P	O	PHE- 124	2.73	162.28	H-Bond (Ligand Donor)	false
C6P	CD1	TYR- 125	4.47	0	Hydrophobic	false
CEP	CG1	ILE- 126	4.14	0	Hydrophobic	false
CAP	CB	ILE- 126	4.37	0	Hydrophobic	false
O9P	N	ILE- 126	2.86	167.43	H-Bond (Protein Donor)	false
CAP	CG	GLN- 131	3.96	0	Hydrophobic	false
C3B	CG	ARG- 132	4.33	0	Hydrophobic	false
C5B	CG	ARG- 132	4.2	0	Hydrophobic	false
O8A	NE	ARG- 132	2.83	151.04	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 132	2.86	173.36	H-Bond (Protein Donor)	false
O5A	N	ARG- 132	2.88	152.81	H-Bond (Protein Donor)	false
O8A	CZ	ARG- 132	3.62	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 132	3.76	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 132	3.59	172.62	Pi/Cation	false
O2A	N	GLY- 134	2.79	145.21	H-Bond (Protein Donor)	false
O4A	N	GLY- 136	2.86	149.96	H-Bond (Protein Donor)	false
O1A	N	ARG- 137	2.91	147.3	H-Bond (Protein Donor)	false
CH3	CG2	ILE- 156	3.91	0	Hydrophobic	false
O5P	OG	SER- 160	2.73	162.21	H-Bond (Protein Donor)	false
C2P	CB	SER- 160	4.03	0	Hydrophobic	false
CDP	CB	LYS- 162	4.12	0	Hydrophobic	false
S1P	CD2	LEU- 163	3.86	0	Hydrophobic	false
CH3	CD2	LEU- 163	3.88	0	Hydrophobic	false
C2B	CB	LYS- 165	4.05	0	Hydrophobic	false
C1B	CB	PHE- 166	3.88	0	Hydrophobic	false
CCP	CD2	PHE- 166	3.7	0	Hydrophobic	false
C4B	CD2	PHE- 166	4.18	0	Hydrophobic	false
O7A	NZ	LYS- 169	2.67	168.06	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 169	2.67	0	Ionic (Protein Cationic)	false
C3B	CD	LYS- 169	4.3	0	Hydrophobic	false
O5B	NE2	HIS- 170	3	161.91	H-Bond (Protein Donor)	false
O4A	O	HOH- 301	2.62	147.42	H-Bond (Protein Donor)	false