scPDB - 4xrb entry

Protein Data Bank Entry:

PDB ID : 4xrb

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-01-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc
ID:	P71968_MYCTU
AC:	P71968
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.636
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.298	442.125

% Hydrophobic	% Polar
45.80	54.20
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	62.73 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
21.3471	16.3288	15.0101

Binding mode :

What is Poseview ?

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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	CE2	PHE- 45	3.51	0	Hydrophobic	false
O7N	N	ILE- 46	2.95	164.78	H-Bond (Protein Donor)	false
N7N	O	ILE- 46	2.75	166.6	H-Bond (Ligand Donor)	false
N7N	O	ALA- 53	2.75	128.36	H-Bond (Ligand Donor)	false
O3D	O	GLY- 57	2.76	171.64	H-Bond (Ligand Donor)	false
O2D	O	GLY- 57	3.18	154.57	H-Bond (Ligand Donor)	false
C1B	CG1	VAL- 85	3.58	0	Hydrophobic	false
O5B	N	GLY- 86	3.07	141.75	H-Bond (Protein Donor)	false
O4B	N	GLY- 86	3.2	149.3	H-Bond (Protein Donor)	false
O2A	N	THR- 87	2.96	140.16	H-Bond (Protein Donor)	false
C1D	CG2	THR- 87	4.26	0	Hydrophobic	false
C5D	CG2	THR- 87	3.56	0	Hydrophobic	false
O1X	OG1	THR- 121	2.88	156.45	H-Bond (Protein Donor)	false
O2X	N	ARG- 122	2.78	128.41	H-Bond (Protein Donor)	false
O1X	OG	SER- 123	3.32	147.47	H-Bond (Protein Donor)	false
O2X	N	SER- 123	3.18	143.68	H-Bond (Protein Donor)	false
N6A	OE2	GLU- 175	2.51	139.07	H-Bond (Ligand Donor)	false
O1A	N	GLY- 195	3.01	127.21	H-Bond (Protein Donor)	false
O2A	N	GLY- 195	2.86	126.36	H-Bond (Protein Donor)	false
C5B	CB	THR- 197	3.57	0	Hydrophobic	false
C3B	CG2	THR- 197	4.5	0	Hydrophobic	false
O3	N	THR- 197	3.47	159.66	H-Bond (Protein Donor)	false
O1A	N	LEU- 198	2.77	164.55	H-Bond (Protein Donor)	false
N6A	OG1	THR- 201	2.85	147.47	H-Bond (Ligand Donor)	false
O3D	NH2	ARG- 225	3.15	174.34	H-Bond (Protein Donor)	false