scPDB - 2y5d entry

Protein Data Bank Entry:

PDB ID : 2y5d

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2011-01-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
ID:	Q13WK4_BURXL
AC:	Q13WK4
Organism:	Burkholderia xenovorans
Reign:	Bacteria
TaxID:	266265
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.692
Number of residues:	53
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.254	941.625

% Hydrophobic	% Polar
50.90	49.10
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	55.63 %
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
-18.3069	-6.78373	-9.35373

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
C1B	CG2	ILE- 155	3.67	0	Hydrophobic	false
C4B	CG2	ILE- 155	3.78	0	Hydrophobic	false
O3B	O	ASN- 156	2.79	156.15	H-Bond (Ligand Donor)	false
C5D	CB	ALA- 157	4.17	0	Hydrophobic	false
C5N	CB	ALA- 157	3.55	0	Hydrophobic	false
C5D	CD2	PHE- 158	3.32	0	Hydrophobic	false
C3D	CE2	PHE- 158	3.54	0	Hydrophobic	false
O3B	NZ	LYS- 182	2.83	173.9	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 182	3.48	121.02	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 182	3.48	0	Ionic (Protein Cationic)	false
C3B	CB	ALA- 184	3.98	0	Hydrophobic	false
O1X	N	THR- 185	3.08	150.34	H-Bond (Protein Donor)	false
O2X	OG1	THR- 185	2.62	166.59	H-Bond (Protein Donor)	false
O2X	N	THR- 185	3.09	147.9	H-Bond (Protein Donor)	false
C1B	CE1	PHE- 231	4.48	0	Hydrophobic	false
C4B	CE1	PHE- 231	3.71	0	Hydrophobic	false
C5N	CG2	THR- 232	3.78	0	Hydrophobic	false
O1A	OG	SER- 234	2.92	163.68	H-Bond (Protein Donor)	false
O1A	N	SER- 234	2.67	173.33	H-Bond (Protein Donor)	false
O2A	OG1	THR- 237	2.77	171.78	H-Bond (Protein Donor)	false
C4N	CB	ALA- 296	3.27	0	Hydrophobic	false
C3D	CD2	PHE- 402	3.77	0	Hydrophobic	false
C2D	CE1	PHE- 402	3.48	0	Hydrophobic	false
O2X	O	HOH- 2405	2.99	144.91	H-Bond (Protein Donor)	false