scPDB - 4xd1 entry

Protein Data Bank Entry:

PDB ID : 4xd1

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2014-12-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Qdtf
ID:	F8RC03_9ENTR
AC:	F8RC03
Organism:	Providencia alcalifaciens
Reign:	Bacteria
TaxID:	126385
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	12.125
Number of residues:	43
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	6
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.688	695.250

% Hydrophobic	% Polar
39.32	60.68
According to VolSite

Ligand :

HET Code:	T3Q
Formula:	C16H26N3O14P2
Molecular weight:	546.337 g/mol
DrugBank ID:	-
Buried Surface Area:	59 %
Polar Surface area:	283.77 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-1.29177	70.7489	20.5875

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
O1A	NZ	LYS- 8	3.3	133.46	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 8	3.3	0	Ionic (Protein Cationic)	false
N3Q	OE2	GLU- 75	3.69	0	Ionic (Ligand Cationic)	false
O4Q	O	PHE- 76	2.65	166.23	H-Bond (Ligand Donor)	false
C6Q	CB	ASP- 77	4.35	0	Hydrophobic	false
O2Q	O	GLY- 103	2.77	152.44	H-Bond (Ligand Donor)	false
C1Q	SD	MET- 104	3.77	0	Hydrophobic	false
O1B	N	TYR- 105	2.82	156.73	H-Bond (Protein Donor)	false
C2'	CD1	TYR- 105	4.44	0	Hydrophobic	false
O3'	N	SER- 107	3.13	157.93	H-Bond (Protein Donor)	false
C3'	CB	SER- 107	4.02	0	Hydrophobic	false
C4'	CD1	TYR- 152	4.06	0	Hydrophobic	false
C5'	CE1	TYR- 152	3.51	0	Hydrophobic	false
C5M	CD2	TYR- 195	4.4	0	Hydrophobic	false
C2'	CZ	TYR- 195	4.21	0	Hydrophobic	false
C1'	CD1	PHE- 218	3.77	0	Hydrophobic	false
C4'	CE1	PHE- 218	3.84	0	Hydrophobic	false
C5M	CE1	TYR- 221	4.07	0	Hydrophobic	false
C1'	CD2	TYR- 221	4.35	0	Hydrophobic	false
N3	OE1	GLN- 222	2.84	174.8	H-Bond (Ligand Donor)	false
O2	NE2	GLN- 222	2.91	170.77	H-Bond (Protein Donor)	false
N3Q	O	HOH- 720	2.79	174.65	H-Bond (Ligand Donor)	false
N3Q	O	HOH- 722	3.02	176.52	H-Bond (Ligand Donor)	false
N3Q	O	HOH- 782	3.2	136.41	H-Bond (Ligand Donor)	false