scPDB - 1vp5 entry

Protein Data Bank Entry:

PDB ID : 1vp5

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxidoreductase, aldo/keto reductase family
ID:	Q9X0A2_THEMA
AC:	Q9X0A2
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.248
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.492	820.125

% Hydrophobic	% Polar
52.26	47.74
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	74.36 %
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
67.2839	18.8352	-35.2435

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
O3D	N	PHE- 22	3.07	151.8	H-Bond (Protein Donor)	false
C3D	CB	PHE- 22	3.52	0	Hydrophobic	false
O2D	OD2	ASP- 45	2.75	160.8	H-Bond (Ligand Donor)	false
C2D	CE2	TYR- 50	4.03	0	Hydrophobic	false
N7N	OG	SER- 140	2.92	150.09	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 141	2.76	172.21	H-Bond (Protein Donor)	false
N7N	OE1	GLN- 162	2.85	156.98	H-Bond (Ligand Donor)	false
C3N	CB	TRP- 188	3.95	0	Hydrophobic	false
C4N	CD2	TRP- 188	3.48	0	Hydrophobic	false
O5D	N	GLY- 189	3.01	139.8	H-Bond (Protein Donor)	false
O2A	N	PHE- 191	2.75	145.86	H-Bond (Protein Donor)	false
C5B	CD2	PHE- 191	4.44	0	Hydrophobic	false
O2A	N	GLU- 193	3.1	159.54	H-Bond (Protein Donor)	false
O2N	OE1	GLU- 193	2.55	158.44	H-Bond (Protein Donor)	false
C1B	CZ	PHE- 199	4.26	0	Hydrophobic	false
C4D	CD1	ILE- 231	3.94	0	Hydrophobic	false
C2D	CD1	ILE- 231	4.42	0	Hydrophobic	false
O1A	N	LYS- 233	3.11	158.7	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 233	2.72	171.98	H-Bond (Protein Donor)	false
C5B	CD	LYS- 233	4.19	0	Hydrophobic	false
C3B	CD	LYS- 233	4.19	0	Hydrophobic	false
C5D	CB	LYS- 233	4.29	0	Hydrophobic	false
C3D	CB	LYS- 233	4.38	0	Hydrophobic	false
O2X	NZ	LYS- 233	2.72	0	Ionic (Protein Cationic)	false
O3X	OG1	THR- 234	2.57	170.37	H-Bond (Protein Donor)	false
O2X	N	VAL- 235	3.05	152.71	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 239	2.96	140.45	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 239	3.89	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 239	3.78	160.55	Pi/Cation	false
N6A	OE2	GLU- 242	3.16	176.44	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 243	3.22	165.24	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 243	2.59	138.42	H-Bond (Ligand Donor)	false