scPDB - 2yw9 entry

Protein Data Bank Entry:

PDB ID : 2yw9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-04-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Enoyl-[acyl-carrier-protein] reductase [NADH]
ID:	Q5SLI9_THET8
AC:	Q5SLI9
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.309
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.408	658.125

% Hydrophobic	% Polar
55.38	44.62
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	64.16 %
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
43.2491	-24.1337	77.4111

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
O3B	OG1	THR- 17	2.96	167.44	H-Bond (Protein Donor)	false
C3B	CG2	THR- 17	4.12	0	Hydrophobic	false
O2A	OG	SER- 21	3.18	142.96	H-Bond (Protein Donor)	false
O2N	N	LEU- 22	2.84	165.69	H-Bond (Protein Donor)	false
C5D	CB	LEU- 22	4.32	0	Hydrophobic	false
C3N	CD1	LEU- 22	3.96	0	Hydrophobic	false
O2B	NE2	GLN- 42	3.05	122.15	H-Bond (Protein Donor)	false
O3X	NE2	GLN- 42	2.82	134.98	H-Bond (Protein Donor)	false
N1A	N	VAL- 67	3.13	174.95	H-Bond (Protein Donor)	false
C5D	CB	ALA- 93	4.19	0	Hydrophobic	false
C1B	CG2	ILE- 94	4.25	0	Hydrophobic	false
C3D	CB	ALA- 95	3.58	0	Hydrophobic	false
C5D	CD1	LEU- 145	4.31	0	Hydrophobic	false
C4D	CB	LEU- 145	3.72	0	Hydrophobic	false
C5N	CB	TYR- 147	3.95	0	Hydrophobic	false
O3D	NZ	LYS- 164	3.12	139.49	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 164	3.08	147.92	H-Bond (Protein Donor)	false
C5N	CB	ALA- 190	3.76	0	Hydrophobic	false
O7N	N	VAL- 193	2.93	168.93	H-Bond (Protein Donor)	false
O3D	O	HOH- 501	2.91	135.64	H-Bond (Ligand Donor)	false