scPDB - 4kvx entry

Protein Data Bank Entry:

PDB ID : 4kvx

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-05-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-terminal acetyltransferase A complex catalytic subunit ard1
ID:	ARD1_SCHPO
AC:	Q9UTI3
Organism:	Schizosaccharomyces pombe
Reign:	Eukaryota
TaxID:	284812
EC Number:	2.3.1.88

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
B	5 %

Ligand binding site composition:

B-Factor:	22.123
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.100	1039.500

% Hydrophobic	% Polar
43.18	56.82
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	61.21 %
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
11.8881	21.5113	28.1109

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	CG	GLU- 24	4.39	0	Hydrophobic	false
CH3	CG2	ILE- 73	4.25	0	Hydrophobic	false
CEP	CG2	VAL- 76	4.19	0	Hydrophobic	false
N4P	O	VAL- 76	2.63	170.99	H-Bond (Ligand Donor)	false
O	N	VAL- 76	3.03	135.99	H-Bond (Protein Donor)	false
C6P	CB	SER- 77	4.25	0	Hydrophobic	false
CEP	CG2	VAL- 78	4.3	0	Hydrophobic	false
O9P	N	VAL- 78	2.85	171.68	H-Bond (Protein Donor)	false
CAP	CD	ARG- 83	4.08	0	Hydrophobic	false
O5A	N	HIS- 84	2.86	152.12	H-Bond (Protein Donor)	false
O1A	N	GLY- 86	2.85	143.77	H-Bond (Protein Donor)	false
O4A	N	ALA- 88	3.4	158.12	H-Bond (Protein Donor)	false
CCP	CB	ALA- 88	3.74	0	Hydrophobic	false
O2A	N	LYS- 89	2.87	165.52	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 97	3.48	143.59	H-Bond (Protein Donor)	false
CH3	CB	LEU- 110	3.94	0	Hydrophobic	false
S1P	CG1	VAL- 112	3.86	0	Hydrophobic	false
O5P	ND2	ASN- 116	2.74	156.81	H-Bond (Protein Donor)	false
CDP	CB	ALA- 118	4.41	0	Hydrophobic	false
CDP	CB	ALA- 119	4.07	0	Hydrophobic	false
C1B	CB	HIS- 121	3.99	0	Hydrophobic	false
C1B	CB	LEU- 122	4.08	0	Hydrophobic	false
C4B	CD1	LEU- 122	4.39	0	Hydrophobic	false
CDP	CD2	LEU- 122	4.46	0	Hydrophobic	false
S1P	CE2	TYR- 123	4.23	0	Hydrophobic	false
CH3	CZ	TYR- 123	4.12	0	Hydrophobic	false
C3B	CG2	THR- 126	3.74	0	Hydrophobic	false