scPDB - 3d7k entry

Protein Data Bank Entry:

PDB ID : 3d7k

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2008-05-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Benzaldehyde lyase
ID:	Q9F4L3_PSEFL
AC:	Q9F4L3
Organism:	Pseudomonas fluorescens
Reign:	Bacteria
TaxID:	294
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	33 %
B	67 %

Ligand binding site composition:

B-Factor:	37.435
Number of residues:	55
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.388	1184.625

% Hydrophobic	% Polar
47.01	52.99
According to VolSite

Ligand :

HET Code:	D7K
Formula:	C20H24N4O11P3S
Molecular weight:	621.411 g/mol
DrugBank ID:	-
Buried Surface Area:	76.3 %
Polar Surface area:	304.71 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-70.4547	15.7207	-3.20197

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
CM4	CD2	LEU- 25	4.4	0	Hydrophobic	false
O12	N	ALA- 28	2.55	164.52	H-Bond (Protein Donor)	false
C10	CB	ALA- 28	4.02	0	Hydrophobic	false
N1,	OE2	GLU- 50	2.64	159.54	H-Bond (Ligand Donor)	false
C5,	CG2	THR- 73	3.74	0	Hydrophobic	false
C10	CD2	LEU- 112	4.24	0	Hydrophobic	false
C6	CD2	LEU- 112	4.19	0	Hydrophobic	false
O7	OE1	GLN- 113	2.59	135.15	H-Bond (Ligand Donor)	false
S1	CB	ALA- 394	3.62	0	Hydrophobic	false
C01	CB	ALA- 394	4.11	0	Hydrophobic	false
O3B	N	LEU- 395	3.08	148.22	H-Bond (Protein Donor)	false
O1B	N	THR- 396	2.91	164.36	H-Bond (Protein Donor)	false
O1B	OG1	THR- 396	2.91	170.68	H-Bond (Protein Donor)	false
N4,	O	GLY- 419	2.82	173.28	H-Bond (Ligand Donor)	false
CM2	CB	SER- 420	4.49	0	Hydrophobic	false
C01	CG	MET- 421	3.83	0	Hydrophobic	false
CM4	CG	MET- 421	4.32	0	Hydrophobic	false
C5,	CG	MET- 421	4.19	0	Hydrophobic	false
CM2	CB	MET- 421	4.45	0	Hydrophobic	false
S1	CE	MET- 421	3.74	0	Hydrophobic	false
C1	CE	MET- 421	3.39	0	Hydrophobic	false
N3,	N	MET- 421	3.09	164.7	H-Bond (Protein Donor)	false
O1A	N	GLY- 449	2.83	143.87	H-Bond (Protein Donor)	false
O2A	N	SER- 450	2.77	140.14	H-Bond (Protein Donor)	false
O2A	OG	SER- 450	2.53	156.39	H-Bond (Protein Donor)	false
CM2	CZ	TYR- 453	3.98	0	Hydrophobic	false
O2B	ND2	ASN- 475	3.16	143.2	H-Bond (Protein Donor)	false
C01	CE3	TRP- 478	3.53	0	Hydrophobic	false
C05	CB	TRP- 478	3.74	0	Hydrophobic	false
CM4	CE3	TRP- 478	3.36	0	Hydrophobic	false
O2B	N	GLY- 479	2.8	137.22	H-Bond (Protein Donor)	false
O3B	N	ALA- 480	3	167.49	H-Bond (Protein Donor)	false
S1	CB	ALA- 480	3.98	0	Hydrophobic	false
C3	CB	ALA- 480	4.16	0	Hydrophobic	false
C05	CG2	THR- 481	4.49	0	Hydrophobic	false
CM4	CG2	THR- 481	4.14	0	Hydrophobic	false
C7,	CG2	THR- 481	4.27	0	Hydrophobic	false
S1	CG2	THR- 481	4.09	0	Hydrophobic	false
O1A	CA	CA- 571	1.98	0	Metal Acceptor	false
O2B	CA	CA- 571	2.14	0	Metal Acceptor	false
O12	O	HOH- 583	2.5	179.98	H-Bond (Protein Donor)	false