scPDB - 5jy1 entry

Protein Data Bank Entry:

PDB ID : 5jy1

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2016-05-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative short-chain dehydrogenase/reductase
ID:	Q13HF0_BURXL
AC:	Q13HF0
Organism:	Burkholderia xenovorans
Reign:	Bacteria
TaxID:	266265
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.925
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.115	1532.250

% Hydrophobic	% Polar
47.58	52.42
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.24 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
8.02445	25.0807	46.6878

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
O2N	N	ILE- 18	2.59	174.87	H-Bond (Protein Donor)	false
C5D	CB	ILE- 18	3.91	0	Hydrophobic	false
C4D	CD1	ILE- 18	4.43	0	Hydrophobic	false
C3N	CD1	ILE- 18	4.25	0	Hydrophobic	false
O3B	OE1	GLU- 37	2.8	157.41	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 37	2.57	168.69	H-Bond (Ligand Donor)	false
N6A	OD1	ASP- 63	2.94	126.9	H-Bond (Ligand Donor)	false
N1A	N	VAL- 64	3.16	168.43	H-Bond (Protein Donor)	false
O3D	O	ASN- 90	2.89	139.99	H-Bond (Ligand Donor)	false
C3D	CB	PHE- 92	3.77	0	Hydrophobic	false
C4D	CD2	PHE- 141	4.21	0	Hydrophobic	false
C5N	CB	SER- 143	3.86	0	Hydrophobic	false
O2D	OH	TYR- 156	2.74	168.21	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 160	3.21	128.53	H-Bond (Protein Donor)	false
C4N	CG2	THR- 187	4.38	0	Hydrophobic	false
O7N	N	ALA- 188	3	160.23	H-Bond (Protein Donor)	false
N7N	O	ALA- 188	3.27	145.14	H-Bond (Ligand Donor)	false
O2A	N	ALA- 191	3.04	162.81	H-Bond (Protein Donor)	false