scPDB - 4hxy entry

Protein Data Bank Entry:

PDB ID : 4hxy

Resolution :1.680 Å

Experimental Method : X-ray

Deposition Date : 2012-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Plm1
ID:	Q6V1M8_9ACTN
AC:	Q6V1M8
Organism:	Streptomyces sp. HK803
Reign:	Bacteria
TaxID:	244967
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.239
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.222	1019.250

% Hydrophobic	% Polar
46.36	53.64
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	74.93 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
7.66046	51.9515	25.0017

Binding mode :

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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	N	GLY- 195	2.9	170.09	H-Bond (Protein Donor)	false
O1N	N	LEU- 196	2.83	172.94	H-Bond (Protein Donor)	false
C5D	CB	LEU- 196	4.04	0	Hydrophobic	false
C3N	CD2	LEU- 196	4.05	0	Hydrophobic	false
O2X	NH2	ARG- 218	2.89	148.9	H-Bond (Protein Donor)	false
O3X	N	ARG- 218	2.81	155.07	H-Bond (Protein Donor)	false
O3X	NE	ARG- 218	2.79	168.88	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 218	3.61	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 218	3.66	0	Ionic (Protein Cationic)	false
O1X	NE2	GLN- 219	2.96	157.53	H-Bond (Protein Donor)	false
O1X	N	GLN- 219	2.91	150.41	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 246	3.02	166.27	H-Bond (Ligand Donor)	false
N1A	N	VAL- 247	2.97	179.38	H-Bond (Protein Donor)	false
C5D	CB	ALA- 273	3.93	0	Hydrophobic	false
C1B	CB	ALA- 274	4.45	0	Hydrophobic	false
O4B	N	GLY- 275	3.41	158.18	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 297	2.8	139.53	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 297	3.13	140.66	H-Bond (Protein Donor)	false
C4D	CB	PHE- 317	4.25	0	Hydrophobic	false
C5N	CB	SER- 319	3.95	0	Hydrophobic	false
O2D	OH	TYR- 332	2.75	157.77	H-Bond (Ligand Donor)	false
C5N	CB	TRP- 358	3.48	0	Hydrophobic	false
O7N	N	TRP- 361	2.8	169.94	H-Bond (Protein Donor)	false
O2N	N	MET- 366	2.8	162.62	H-Bond (Protein Donor)	false
C2D	CE	MET- 366	3.55	0	Hydrophobic	false
O5B	O	HOH- 602	3.24	166.21	H-Bond (Protein Donor)	false