scPDB - 3rq8 entry

Protein Data Bank Entry:

PDB ID : 3rq8

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-04-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-dependent (S)-NAD(P)H-hydrate dehydratase
ID:	NNRD_BACSU
AC:	P94368
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.158
Number of residues:	50
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.238	408.375

% Hydrophobic	% Polar
35.54	64.46
According to VolSite

Ligand :

HET Code:	AP5
Formula:	C20H24N10O22P5
Molecular weight:	911.327 g/mol
DrugBank ID:	DB01717
Buried Surface Area:	43 %
Polar Surface area:	543.69 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
12.8692	-23.097	-23.9749

Binding mode :

What is Poseview ?

2D View
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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	NZ	LYS- 186	2.71	164.43	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 186	2.71	0	Ionic (Protein Cationic)	false
C3F	CG	LYS- 186	3.86	0	Hydrophobic	false
C2F	CB	LYS- 186	3.86	0	Hydrophobic	false
O2F	N	GLY- 187	2.9	160.95	H-Bond (Protein Donor)	false
C1F	CB	LEU- 209	3.71	0	Hydrophobic	false
O2B	N	GLY- 213	3.03	125.36	H-Bond (Protein Donor)	false
O3B	N	GLY- 213	3.25	166.08	H-Bond (Protein Donor)	false
C4F	CB	THR- 214	4.13	0	Hydrophobic	false
O2B	N	GLY- 215	2.87	127.32	H-Bond (Protein Donor)	false
O2B	N	ASP- 216	3.22	154.85	H-Bond (Protein Donor)	false
O2A	MG	MG- 277	2.01	0	Metal Acceptor	false
O1B	MG	MG- 277	1.96	0	Metal Acceptor	false
O1D	O	HOH- 383	2.79	180	H-Bond (Protein Donor)	false