scPDB - 4y0k entry

Protein Data Bank Entry:

PDB ID : 4y0k

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2015-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	AntE
ID:	M1SQA1_9ACTN
AC:	M1SQA1
Organism:	Streptomyces sp. NRRL 2288
Reign:	Bacteria
TaxID:	1298930
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.688
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.049	813.375

% Hydrophobic	% Polar
36.93	63.07
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	59.67 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
17.2159	-23.3019	-7.93925

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
O2A	OH	TYR- 68	2.88	147.87	H-Bond (Protein Donor)	false
C3D	CD2	TYR- 68	3.92	0	Hydrophobic	false
C2D	CG	TYR- 68	4.25	0	Hydrophobic	false
C4N	CG2	THR- 190	3.57	0	Hydrophobic	false
O1A	N	GLY- 217	2.9	163.9	H-Bond (Protein Donor)	false
O2N	N	LEU- 218	3.04	166.8	H-Bond (Protein Donor)	false
C5D	CD2	LEU- 218	4.06	0	Hydrophobic	false
C5N	CD1	LEU- 218	3.7	0	Hydrophobic	false
O2X	N	SER- 238	2.99	137.89	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 242	3.2	163.01	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 242	3.44	127.97	H-Bond (Protein Donor)	false
O2X	NE	ARG- 242	2.69	175.03	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 242	3.5	0	Ionic (Protein Cationic)	false
O1X	CZ	ARG- 257	3.73	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 257	3.68	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 257	2.92	158.41	H-Bond (Protein Donor)	false
O3X	NE	ARG- 257	2.81	171.31	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 257	3.42	170.86	Pi/Cation	false
C4D	CB	HIS- 305	3.8	0	Hydrophobic	false
N1A	OG	SER- 306	3.27	124.8	H-Bond (Protein Donor)	false
C3N	SG	CYS- 327	4.15	0	Hydrophobic	false
N7N	O	CYS- 327	2.95	149.37	H-Bond (Ligand Donor)	false
O3D	OG1	THR- 330	2.75	138.21	H-Bond (Ligand Donor)	false
N7N	ND1	HIS- 353	2.94	164.63	H-Bond (Ligand Donor)	false
O7N	N	VAL- 354	3.01	144.36	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 397	2.72	144.07	H-Bond (Protein Donor)	false
O5B	O	HOH- 649	3.4	167.01	H-Bond (Protein Donor)	false