scPDB - 3mk6 entry

Protein Data Bank Entry:

PDB ID : 3mk6

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2010-04-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pantothenate kinase 3
ID:	PANK3_HUMAN
AC:	Q9H999
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.33

Chains:

Chain Name:	Percentage of Residues within binding site
A	32 %
C	68 %

Ligand binding site composition:

B-Factor:	29.328
Number of residues:	61
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.033	1356.750

% Hydrophobic	% Polar
39.80	60.20
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	63.91 %
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
-16.5631	-35.0894	6.21427

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
O8A	OD2	ASP- 17	2.59	158.85	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 24	3.73	0	Ionic (Protein Cationic)	false
O2B	N	GLY- 116	2.81	164.38	H-Bond (Protein Donor)	false
N1A	NZ	LYS- 135	2.81	169.33	H-Bond (Protein Donor)	false
C1B	CG	GLU- 138	3.89	0	Hydrophobic	false
C4B	CG	GLU- 138	4.4	0	Hydrophobic	false
O1A	N	SER- 192	2.83	161.99	H-Bond (Protein Donor)	false
O4A	OG	SER- 192	2.62	159.46	H-Bond (Protein Donor)	false
O4A	N	GLY- 193	2.91	164.82	H-Bond (Protein Donor)	false
CEP	CB	SER- 195	4.45	0	Hydrophobic	false
O9P	OG	SER- 195	2.59	136.96	H-Bond (Protein Donor)	false
O9P	NH2	ARG- 207	2.86	155.73	H-Bond (Protein Donor)	false
O5P	NH2	ARG- 207	2.77	153.08	H-Bond (Protein Donor)	false
C2P	CB	SER- 212	4.21	0	Hydrophobic	false
CDP	CG2	VAL- 250	3.97	0	Hydrophobic	false
CCP	CD1	ILE- 253	3.74	0	Hydrophobic	false
CDP	CD1	ILE- 253	4.43	0	Hydrophobic	false
CCP	CE2	TYR- 254	4.36	0	Hydrophobic	false
CDP	CE2	TYR- 254	4.11	0	Hydrophobic	false
CEP	CE2	TYR- 258	4.3	0	Hydrophobic	false
CDP	CD1	LEU- 263	3.85	0	Hydrophobic	false
CEP	CD1	LEU- 263	4.36	0	Hydrophobic	false
C6P	CD2	LEU- 263	4.05	0	Hydrophobic	false
N4P	O	VAL- 268	2.82	159.3	H-Bond (Ligand Donor)	false
C2P	CB	VAL- 268	4.22	0	Hydrophobic	false
O	N	VAL- 268	2.81	171.4	H-Bond (Protein Donor)	false
CDP	CB	ALA- 269	3.84	0	Hydrophobic	false
N8P	O	ALA- 269	3.16	151.53	H-Bond (Ligand Donor)	false
S1P	CB	ASN- 299	4.01	0	Hydrophobic	false
O7A	CZ	ARG- 325	3.52	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 325	3.95	0	Ionic (Protein Cationic)	false
O7A	NH1	ARG- 325	3.34	132.65	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 325	2.82	159.44	H-Bond (Protein Donor)	false
O9A	NH1	ARG- 325	3	158	H-Bond (Protein Donor)	false
CH3	CE2	TYR- 336	3.83	0	Hydrophobic	false
CH3	CD2	TYR- 340	3.5	0	Hydrophobic	false
S1P	CE2	TYR- 340	3.74	0	Hydrophobic	false
S1P	CZ2	TRP- 341	3.37	0	Hydrophobic	false
O3B	O	HOH- 400	3.05	179.95	H-Bond (Protein Donor)	false
O5P	O	HOH- 469	2.9	160.6	H-Bond (Protein Donor)	false