scPDB - 2vrb entry

Protein Data Bank Entry:

PDB ID : 2vrb

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-03-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Triphenylmethane reductase
ID:	Q2TNI4_9ENTR
AC:	Q2TNI4
Organism:	Citrobacter sp. MY-5
Reign:	Bacteria
TaxID:	308866
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.443
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.396	934.875

% Hydrophobic	% Polar
57.40	42.60
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	56.87 %
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
6.10725	27.1015	2.03256

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
O1X	OG1	THR- 9	3.13	144.16	H-Bond (Protein Donor)	false
O2A	N	GLN- 11	2.98	170.14	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 11	3.32	164.59	H-Bond (Protein Donor)	false
O1N	N	LEU- 12	2.59	168.65	H-Bond (Protein Donor)	false
C5D	CB	LEU- 12	3.95	0	Hydrophobic	false
O2X	CZ	ARG- 34	3.83	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 34	2.84	158.96	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 53	3.05	145.91	H-Bond (Ligand Donor)	false
N1A	N	TYR- 54	2.95	171.36	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 73	3.56	0	Hydrophobic	false
O2D	OG	SER- 74	3.16	126.83	H-Bond (Protein Donor)	false
O2D	O	GLY- 75	2.53	137.53	H-Bond (Ligand Donor)	false
C1B	CG	PRO- 76	4.48	0	Hydrophobic	false
C5B	CG	PRO- 76	3.5	0	Hydrophobic	false
C3D	CB	PRO- 76	4.18	0	Hydrophobic	false
N7N	O	ALA- 141	2.99	160.89	H-Bond (Ligand Donor)	false
O5D	OH	TYR- 143	2.87	167.79	H-Bond (Protein Donor)	false
O7N	N	TYR- 143	2.66	140.07	H-Bond (Protein Donor)	false
C3N	CE2	TYR- 143	3.22	0	Hydrophobic	false
O2N	NE	ARG- 175	2.76	143.16	H-Bond (Protein Donor)	false
O2N	NH2	ARG- 175	3.28	125.23	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 175	3.41	0	Ionic (Protein Cationic)	false
N6A	O	HOH- 2017	3.2	163.3	H-Bond (Ligand Donor)	false