scPDB - 1pdh entry

Protein Data Bank Entry:

PDB ID : 1pdh

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1994-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	p-hydroxybenzoate hydroxylase
ID:	PHHY_PSEFL
AC:	P00438
Organism:	Pseudomonas fluorescens
Reign:	Bacteria
TaxID:	294
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.142
Number of residues:	66
Including
Standard Amino Acids:	58
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.851	732.375

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	FAS
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	-
Buried Surface Area:	59.76 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
24.1875	97.3972	58.2588

Binding mode :

What is Poseview ?

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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
C4'	CG	PRO- 12	4.47	0	Hydrophobic	false
O1P	OG	SER- 13	2.97	168.32	H-Bond (Protein Donor)	false
O2P	N	SER- 13	3.01	156.42	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 32	2.62	135.22	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 32	3.23	158.51	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 32	2.59	151.11	H-Bond (Ligand Donor)	false
N3A	N	ARG- 33	3.05	149.66	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 42	2.95	155.2	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 42	3.15	146.82	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 44	3.11	160.61	H-Bond (Protein Donor)	false
O4'	NH1	ARG- 44	2.88	149.9	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 44	3.97	0	Ionic (Protein Cationic)	false
C6	CG	ARG- 44	3.9	0	Hydrophobic	false
C2'	CD	ARG- 44	4.01	0	Hydrophobic	false
C9	CD	ARG- 44	3.8	0	Hydrophobic	false
O2'	OE1	GLN- 102	2.68	162.16	H-Bond (Ligand Donor)	false
O4'	NE2	GLN- 102	2.84	149.88	H-Bond (Protein Donor)	false
C1B	CB	ASP- 159	4.33	0	Hydrophobic	false
C6	CB	ALA- 266	4.13	0	Hydrophobic	false
C7M	CB	ALA- 266	4.42	0	Hydrophobic	false
O3'	OD1	ASP- 286	2.93	169.58	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 286	3.46	120.82	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 286	4.15	0	Hydrophobic	false
O1P	N	ASP- 286	3.06	156.44	H-Bond (Protein Donor)	false
O2P	O	HOH- 407	2.72	177.95	H-Bond (Protein Donor)	false
O1P	O	HOH- 493	2.69	179.96	H-Bond (Protein Donor)	false
O1A	O	HOH- 495	2.68	179.97	H-Bond (Protein Donor)	false
N1A	O	HOH- 506	3.03	179.97	H-Bond (Protein Donor)	false
O2	O	HOH- 552	3.13	179.96	H-Bond (Protein Donor)	false
N5	O	HOH- 622	3.03	154.37	H-Bond (Protein Donor)	false