scPDB - 1kv9 entry

Protein Data Bank Entry:

PDB ID : 1kv9

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2002-01-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinohemoprotein alcohol dehydrogenase ADH IIB
ID:	QHED_PSEPU
AC:	Q8GR64
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.501
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.437	263.250

% Hydrophobic	% Polar
53.85	46.15
According to VolSite

Ligand :

HET Code:	PQQ
Formula:	C14H3N2O8
Molecular weight:	327.182 g/mol
DrugBank ID:	DB03205
Buried Surface Area:	83.57 %
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
2.35133	-2.24812	8.03558

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
O2B	OE1	GLU- 59	3.18	128.73	H-Bond (Protein Donor)	false
C9	SG	CYS- 105	3.6	0	Hydrophobic	false
C5	SG	CYS- 106	4.28	0	Hydrophobic	false
C1A	SG	CYS- 106	3.27	0	Hydrophobic	false
C9A	SG	CYS- 106	3.49	0	Hydrophobic	false
O2A	NH2	ARG- 111	3.27	141.59	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 111	2.84	154.76	H-Bond (Protein Donor)	false
O9A	CZ	ARG- 111	3.89	0	Ionic (Protein Cationic)	false
O9A	OG1	THR- 155	3.15	141.29	H-Bond (Protein Donor)	false
O9B	OG1	THR- 155	2.61	149.01	H-Bond (Protein Donor)	false
O7B	N	GLY- 171	2.81	158.04	H-Bond (Protein Donor)	false
O7B	N	ALA- 172	3.05	166.05	H-Bond (Protein Donor)	false
O7B	OG1	THR- 230	2.53	159.69	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 232	3.57	0	Aromatic Face/Face	false
DuAr	DuAr	TRP- 232	3.82	0	Aromatic Face/Face	false
C8	CB	TRP- 232	3.92	0	Hydrophobic	false
O5	NZ	LYS- 322	2.66	151.26	H-Bond (Protein Donor)	false
O4	ND2	ASN- 382	2.89	170.3	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 383	2.56	122.77	H-Bond (Protein Donor)	false
O2B	N	VAL- 525	3.26	149.37	H-Bond (Protein Donor)	false
C3A	CG1	VAL- 525	4.22	0	Hydrophobic	false
O5	CA	CA- 802	2.32	0	Metal Acceptor	false
N6	CA	CA- 802	2.46	0	Metal Acceptor	false
O7A	CA	CA- 802	2.44	0	Metal Acceptor	false
DuAr	CA	CA- 802	3.83	99.73	Pi/Cation	false
O7B	O	HOH- 1034	3.35	152.92	H-Bond (Protein Donor)	false
O7A	O	HOH- 1210	2.74	136.89	H-Bond (Protein Donor)	false