scPDB - 2rir entry

Protein Data Bank Entry:

PDB ID : 2rir

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2007-10-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dipicolinate synthase subunit A
ID:	DPAA_BACSU
AC:	Q04809
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:	28.063
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.824	702.000

% Hydrophobic	% Polar
47.12	52.88
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	53.42 %
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
181.683	20.6207	59.4434

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
C4N	CG2	THR- 136	3.98	0	Hydrophobic	false
O3	N	ARG- 164	3.15	131.29	H-Bond (Protein Donor)	false
O3	NE	ARG- 164	3.14	173.15	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 164	3.28	0	Ionic (Protein Cationic)	false
O1N	OG1	THR- 165	2.67	148.34	H-Bond (Protein Donor)	false
O1N	N	THR- 165	2.67	145.5	H-Bond (Protein Donor)	false
C5N	CG2	THR- 165	4.02	0	Hydrophobic	false
O3X	CZ	ARG- 185	3.54	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 185	3.76	153.93	Pi/Cation	false
C1B	CD	ARG- 185	4.3	0	Hydrophobic	false
O3B	NE2	HIS- 189	3.43	149.17	H-Bond (Protein Donor)	false
C5B	CG2	THR- 219	4.48	0	Hydrophobic	false
C5D	CG2	THR- 219	3.98	0	Hydrophobic	false
C1B	CG1	ILE- 220	3.87	0	Hydrophobic	false
C3D	CG	PRO- 221	4.33	0	Hydrophobic	false
O3D	N	SER- 244	3.32	167.45	H-Bond (Protein Donor)	false
O2D	OG	SER- 244	2.52	164.06	H-Bond (Protein Donor)	false
N7N	O	ALA- 264	2.67	136.93	H-Bond (Ligand Donor)	false
O7N	N	LEU- 267	3.25	142.8	H-Bond (Protein Donor)	false