scPDB - 4cvb entry

Protein Data Bank Entry:

PDB ID : 4cvb

Resolution :1.720 Å

Experimental Method : X-ray

Deposition Date : 2014-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alcohol dehydrogenase
ID:	Q93RE9_9BACT
AC:	Q93RE9
Organism:	Pseudogluconobacter saccharoketogenes
Reign:	Bacteria
TaxID:	133921
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.028
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.760	411.750

% Hydrophobic	% Polar
54.92	45.08
According to VolSite

Ligand :

HET Code:	PQQ
Formula:	C14H3N2O8
Molecular weight:	327.182 g/mol
DrugBank ID:	DB03205
Buried Surface Area:	77.25 %
Polar Surface area:	183.21 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
20.0295	38.6586	18.3515

Binding mode :

What is Poseview ?

2D View
3D View

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
C1A	CD2	LEU- 153	4.23	0	Hydrophobic	false
C9	CD1	LEU- 153	3.45	0	Hydrophobic	false
O9B	NH2	ARG- 158	3.02	141.37	H-Bond (Protein Donor)	false
O9A	OG	SER- 203	2.58	167.31	H-Bond (Protein Donor)	false
O7A	OG1	THR- 218	2.61	154.99	H-Bond (Protein Donor)	false
C8	CB	THR- 218	3.77	0	Hydrophobic	false
C8	CB	TRP- 270	4.14	0	Hydrophobic	false
DuAr	DuAr	TRP- 270	3.47	0	Aromatic Face/Face	false
DuAr	DuAr	TRP- 270	3.88	0	Aromatic Face/Face	false
O5	NZ	LYS- 378	2.7	170.12	H-Bond (Protein Donor)	false
O4	OD2	ASP- 439	3.06	120.07	H-Bond (Ligand Donor)	false
O2A	NE1	TRP- 440	2.68	151.36	H-Bond (Protein Donor)	false
O2A	OH	TYR- 515	2.79	164.8	H-Bond (Protein Donor)	false
O5	CA	CA- 1607	2.31	0	Metal Acceptor	false
N6	CA	CA- 1607	2.27	0	Metal Acceptor	false
O7B	CA	CA- 1607	2.52	0	Metal Acceptor	false
DuAr	CA	CA- 1607	3.56	92.99	Pi/Cation	false
O7A	O	HOH- 2290	2.54	146.94	H-Bond (Protein Donor)	false