scPDB - 4kvm entry

Protein Data Bank Entry:

PDB ID : 4kvm

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2013-05-22

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
C	6 %
G	94 %

Ligand binding site composition:

B-Factor:	99.999
Number of residues:	49
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.250	1451.250

% Hydrophobic	% Polar
39.53	60.47
According to VolSite

Ligand :

HET Code:	SER_ALA_SER_GLU_1XE
Formula:	C37H51N11O25P3S
Molecular weight:	1174.846 g/mol
DrugBank ID:	-
Buried Surface Area:	45.97 %
Polar Surface area:	630.57 Å2

Number of
H-Bond Acceptors:	29
H-Bond Donors:	11
Rings:	3
Aromatic rings:	3
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	34

Mass center Coordinates

X	Y	Z
-29.8363	-14.4061	-145.041

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
CB	CD1	LEU- 22	4.33	0	Hydrophobic	false
C6P	CD2	LEU- 22	3.88	0	Hydrophobic	false
C2P	CD2	LEU- 22	4.11	0	Hydrophobic	false
CB	CG	GLU- 24	3.7	0	Hydrophobic	false
N	OH	TYR- 26	3.41	120.86	H-Bond (Ligand Donor)	false
O	OH	TYR- 26	2.82	163.45	H-Bond (Protein Donor)	false
CB	CD1	TYR- 26	4.02	0	Hydrophobic	false
N	O	THR- 74	2.8	157.51	H-Bond (Ligand Donor)	false
CB	CB	THR- 74	4.18	0	Hydrophobic	false
C1	CG1	VAL- 76	4.27	0	Hydrophobic	false
O21	N	VAL- 76	3.1	137.87	H-Bond (Protein Donor)	false
CEP	CG2	VAL- 78	4.2	0	Hydrophobic	false
O9P	N	VAL- 78	3.16	143.09	H-Bond (Protein Donor)	false
CAP	CD	ARG- 83	3.92	0	Hydrophobic	false
O4A	N	HIS- 84	2.59	159.81	H-Bond (Protein Donor)	false
O5A	N	GLY- 86	3.44	150.88	H-Bond (Protein Donor)	false
O5A	N	ALA- 88	3.25	177.7	H-Bond (Protein Donor)	false
CCP	CB	ALA- 88	3.53	0	Hydrophobic	false
O2A	N	LYS- 89	3.48	128.1	H-Bond (Protein Donor)	false
N	O	HIS- 111	2.9	138.92	H-Bond (Ligand Donor)	false
S1P	CG1	VAL- 112	3.47	0	Hydrophobic	false
N4P	OD1	ASN- 116	3.42	125.67	H-Bond (Ligand Donor)	false
CDP	CB	ALA- 118	4.17	0	Hydrophobic	false
S1P	CB	ALA- 119	3.78	0	Hydrophobic	false
CCP	CD2	LEU- 122	4.14	0	Hydrophobic	false
CDP	CD2	LEU- 122	4.33	0	Hydrophobic	false
C1	CE2	TYR- 123	4.04	0	Hydrophobic	false
N	OH	TYR- 138	3.18	135.51	H-Bond (Ligand Donor)	false
CB	CE2	TYR- 138	3.74	0	Hydrophobic	false
O	OH	TYR- 139	3.39	139.96	H-Bond (Protein Donor)	false