scPDB - 2zrf entry

Protein Data Bank Entry:

PDB ID : 2zrf

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2008-08-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein RecA
ID:	RECA_MYCS2
AC:	Q59560
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.526
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.330	432.000

% Hydrophobic	% Polar
39.06	60.94
According to VolSite

Ligand :

HET Code:	DTP
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB03222
Buried Surface Area:	54.86 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-20.0134	19.9523	-11.9066

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
O3B	N	SER- 71	3.1	143.29	H-Bond (Protein Donor)	false
O2B	OG	SER- 72	3.01	171.18	H-Bond (Protein Donor)	false
O2B	N	GLY- 73	2.72	123.67	H-Bond (Protein Donor)	false
O3A	N	GLY- 73	2.81	146.18	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 74	2.53	138.2	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 74	2.81	125.08	H-Bond (Protein Donor)	false
O2B	N	LYS- 74	3.17	158.65	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 74	2.53	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 74	2.81	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 74	3.76	0	Ionic (Protein Cationic)	false
O1G	OG1	THR- 75	3.32	156.22	H-Bond (Protein Donor)	false
O1B	OG1	THR- 75	3.49	124.57	H-Bond (Protein Donor)	false
O2A	N	THR- 76	3.41	148.72	H-Bond (Protein Donor)	false
C1'	CZ	TYR- 105	4.06	0	Hydrophobic	false
O3'	NH1	ARG- 229	3.11	158.36	H-Bond (Protein Donor)	false
C4'	CG2	ILE- 264	4.34	0	Hydrophobic	false
C1'	CG2	ILE- 264	4.4	0	Hydrophobic	false
N3	N	GLY- 267	3.36	156.54	H-Bond (Protein Donor)	false