scPDB - 2vut entry

Protein Data Bank Entry:

PDB ID : 2vut

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-05-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nitrogen metabolite repression protein nmrA
ID:	NMRA_EMENI
AC:	Q5AU62
Organism:	Emericella nidulans
Reign:	Eukaryota
TaxID:	227321
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.653
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.756	749.250

% Hydrophobic	% Polar
40.99	59.01
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	57.69 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
8.77343	-106.73	171.829

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
O4B	ND2	ASN- 12	2.88	146.56	H-Bond (Protein Donor)	false
O3B	OG1	THR- 14	3.16	163.36	H-Bond (Protein Donor)	false
O2A	N	ARG- 16	3.12	151.34	H-Bond (Protein Donor)	false
O2A	NE	ARG- 16	2.8	146.36	H-Bond (Protein Donor)	false
O3	N	ARG- 16	3.49	148.8	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 16	3.68	0	Ionic (Protein Cationic)	false
O1N	N	GLN- 17	2.93	177.32	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 37	3.84	0	Aromatic Face/Face	false
O5D	ND2	ASN- 80	3.03	128.83	H-Bond (Protein Donor)	false
O3D	O	THR- 81	3.47	164.18	H-Bond (Ligand Donor)	false
C5B	CG2	THR- 82	4.5	0	Hydrophobic	false
C5D	CG2	THR- 82	3.53	0	Hydrophobic	false
N7A	OG1	THR- 82	3.31	126.94	H-Bond (Protein Donor)	false
C5N	CE	MET- 113	3.72	0	Hydrophobic	false
C5N	CB	ALA- 150	3.58	0	Hydrophobic	false
O7N	N	TYR- 153	2.74	149.89	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 156	3.08	154.93	H-Bond (Protein Donor)	false
N7N	OD1	ASN- 156	3.21	163.57	H-Bond (Ligand Donor)	false
O1N	O	HOH- 2014	2.74	147.87	H-Bond (Protein Donor)	false