scPDB - 3rqq entry

Protein Data Bank Entry:

PDB ID : 3rqq

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2011-04-28

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:	21.503
Number of residues:	40
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.445	374.625

% Hydrophobic	% Polar
38.74	61.26
According to VolSite

Ligand :

HET Code:	BA3
Formula:	C20H24N10O16P3
Molecular weight:	753.383 g/mol
DrugBank ID:	DB01690
Buried Surface Area:	60.55 %
Polar Surface area:	425.36 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-22.4517	-10.3792	-27.6822

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
O1E	ND1	HIS- 149	3.22	139.77	H-Bond (Protein Donor)	false
C5B	CD	LYS- 186	4.46	0	Hydrophobic	false
C3B	CG	LYS- 186	3.72	0	Hydrophobic	false
C2B	CB	LYS- 186	3.72	0	Hydrophobic	false
O2E	NZ	LYS- 186	2.72	170.88	H-Bond (Protein Donor)	false
O2E	NZ	LYS- 186	2.72	0	Ionic (Protein Cationic)	false
O2B	N	GLY- 187	2.88	149.62	H-Bond (Protein Donor)	false
C1B	CB	LEU- 209	3.63	0	Hydrophobic	false
O1F	N	GLY- 213	3.07	123.41	H-Bond (Protein Donor)	false
O2F	N	GLY- 213	3.12	170.18	H-Bond (Protein Donor)	false
C4B	CB	THR- 214	4.14	0	Hydrophobic	false
O3E	N	GLY- 215	3.36	135.14	H-Bond (Protein Donor)	false
O1F	N	GLY- 215	2.88	127.08	H-Bond (Protein Donor)	false
O1F	N	ASP- 216	3.13	145.7	H-Bond (Protein Donor)	false
O2E	MG	MG- 277	1.98	0	Metal Acceptor	false
O3F	MG	MG- 277	1.91	0	Metal Acceptor	false