scPDB - 1ykf entry

Protein Data Bank Entry:

PDB ID : 1ykf

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1996-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADP-dependent isopropanol dehydrogenase
ID:	ADH_THEBR
AC:	P14941
Organism:	Thermoanaerobacter brockii
Reign:	Bacteria
TaxID:	29323
EC Number:	1.1.1.80

Chains:

Chain Name:	Percentage of Residues within binding site
C	98 %
D	2 %

Ligand binding site composition:

B-Factor:	35.341
Number of residues:	49
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.101	826.875

% Hydrophobic	% Polar
45.31	54.69
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	56.92 %
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
30.5251	45.0216	-1.15233

Binding mode :

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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
O1N	OG1	THR- 38	3.47	169.2	H-Bond (Protein Donor)	false
C2D	CB	THR- 38	4.34	0	Hydrophobic	false
N7N	OD1	ASP- 150	2.75	158.3	H-Bond (Ligand Donor)	false
C5N	CG2	THR- 154	3.29	0	Hydrophobic	false
O3B	N	ILE- 175	2.66	132.71	H-Bond (Protein Donor)	false
O2N	N	VAL- 178	3.03	149.66	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 178	3.81	0	Hydrophobic	false
C5N	CG2	VAL- 178	3.55	0	Hydrophobic	false
O2X	OG	SER- 199	2.98	140.96	H-Bond (Protein Donor)	false
O2X	N	SER- 199	2.99	146.95	H-Bond (Protein Donor)	false
O2X	N	ARG- 200	3.01	160.62	H-Bond (Protein Donor)	false
O3X	NE	ARG- 200	3.18	152.08	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 200	3.9	0	Ionic (Protein Cationic)	false
O2B	OH	TYR- 218	3.04	156.11	H-Bond (Protein Donor)	false
O3D	OD1	ASN- 266	3.03	164.11	H-Bond (Ligand Donor)	false
O4D	N	TYR- 267	3.28	142.04	H-Bond (Protein Donor)	false
C2D	CB	TYR- 267	4.02	0	Hydrophobic	false
DuAr	ZN	ZN- 354	3.84	40.75	Pi/Cation	false