scPDB - 4k9o entry

Protein Data Bank Entry:

PDB ID : 4k9o

Resolution :1.890 Å

Experimental Method : X-ray

Deposition Date : 2013-04-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Benzoylformate decarboxylase
ID:	MDLC_PSEPU
AC:	P20906
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	4.1.1.7

Chains:

Chain Name:	Percentage of Residues within binding site
B	71 %
D	29 %

Ligand binding site composition:

B-Factor:	35.681
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.320	1410.750

% Hydrophobic	% Polar
48.33	51.67
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	81.08 %
Polar Surface area:	225.32 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-35.9547	-10.1778	4.43404

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
N1'	OD1	ASN- 23	3.25	120.55	H-Bond (Ligand Donor)	false
N1'	OE2	GLU- 47	2.74	147.75	H-Bond (Ligand Donor)	false
C5'	CB	HIS- 70	4.06	0	Hydrophobic	false
CM2	CB	ALA- 73	4.33	0	Hydrophobic	false
S1	CG2	THR- 377	3.68	0	Hydrophobic	false
C7	CG2	THR- 377	4.28	0	Hydrophobic	false
O3A	OG1	THR- 377	3.36	161.38	H-Bond (Protein Donor)	false
O3A	N	THR- 377	3.48	140.57	H-Bond (Protein Donor)	false
O2B	N	SER- 378	2.67	153.62	H-Bond (Protein Donor)	false
N4'	O	GLY- 401	2.62	176.3	H-Bond (Ligand Donor)	false
CM2	CB	LEU- 403	4.14	0	Hydrophobic	false
C5'	CD1	LEU- 403	4.07	0	Hydrophobic	false
S1	CD1	LEU- 403	4.19	0	Hydrophobic	false
CM4	CD1	LEU- 403	4.32	0	Hydrophobic	false
C7	CD1	LEU- 403	3.99	0	Hydrophobic	false
N3'	N	LEU- 403	3.26	178.72	H-Bond (Protein Donor)	false
O2A	N	GLY- 429	3.25	154.51	H-Bond (Protein Donor)	false
O1A	N	SER- 430	2.9	140.03	H-Bond (Protein Donor)	false
CM2	CE2	TYR- 433	3.61	0	Hydrophobic	false
O1B	ND2	ASN- 455	3.2	159.28	H-Bond (Protein Donor)	false
CM4	CD1	TYR- 458	4.01	0	Hydrophobic	false
C6	CD1	TYR- 458	3.35	0	Hydrophobic	false
O1B	N	GLY- 459	3	125.72	H-Bond (Protein Donor)	false
S1	CB	ALA- 460	4.43	0	Hydrophobic	false
O3B	N	ALA- 460	2.66	161.54	H-Bond (Protein Donor)	false
CM4	CD1	LEU- 461	3.39	0	Hydrophobic	false
C6	CG	LEU- 461	4.38	0	Hydrophobic	false
O2A	CA	CA- 601	2.01	0	Metal Acceptor	false
O1B	CA	CA- 601	2.1	0	Metal Acceptor	false