scPDB - 1d7l entry

Protein Data Bank Entry:

PDB ID : 1d7l

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-10-18

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_PSEAE
AC:	P20586
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.507
Number of residues:	67
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.091	1255.500

% Hydrophobic	% Polar
37.90	62.10
According to VolSite

Ligand :

HET Code:	RFL
Formula:	C28H34N10O15P2
Molecular weight:	812.575 g/mol
DrugBank ID:	DB03482
Buried Surface Area:	66.64 %
Polar Surface area:	384.94 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
22.7771	96.2245	57.0082

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
OF1	N	SER- 13	2.92	163.07	H-Bond (Protein Donor)	false
OF2	OG	SER- 13	2.93	169.83	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 32	2.61	159.1	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 32	2.62	165.85	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 32	3.35	127.79	H-Bond (Ligand Donor)	false
N3	N	ARG- 33	3.17	150.57	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 42	2.74	135.39	H-Bond (Protein Donor)	false
OA2	NH2	ARG- 44	3.13	147.66	H-Bond (Protein Donor)	false
O4R	NH2	ARG- 44	3.01	155.4	H-Bond (Protein Donor)	false
C8F	CG	ARG- 44	4.23	0	Hydrophobic	false
CM1	CG	ARG- 44	3.91	0	Hydrophobic	false
CM2	CD	ARG- 44	4.05	0	Hydrophobic	false
C9F	CB	ARG- 44	4.05	0	Hydrophobic	false
O4F	N	GLY- 46	3.13	173.77	H-Bond (Protein Donor)	false
N3F	O	VAL- 47	3.12	144.14	H-Bond (Ligand Donor)	false
O4F	N	VAL- 47	3.08	168.08	H-Bond (Protein Donor)	false
O4R	NE2	GLN- 102	3	147.45	H-Bond (Protein Donor)	false
O2R	OE1	GLN- 102	2.55	160.42	H-Bond (Ligand Donor)	false
C1'	CB	ASP- 159	4.33	0	Hydrophobic	false
C7M	CE3	TRP- 185	4.42	0	Hydrophobic	false
C7M	CE1	TYR- 222	3.67	0	Hydrophobic	false
CM1	CB	ALA- 266	3.85	0	Hydrophobic	false
C7M	CB	ALA- 266	4.26	0	Hydrophobic	false
OF2	N	ASP- 286	3.12	146	H-Bond (Protein Donor)	false
C5R	CB	ASP- 286	4.12	0	Hydrophobic	false
O3R	OD1	ASP- 286	2.83	161.01	H-Bond (Ligand Donor)	false
C9A	CB	PRO- 293	4.46	0	Hydrophobic	false
C6F	CB	PRO- 293	3.75	0	Hydrophobic	false
C7F	CG	PRO- 293	3.94	0	Hydrophobic	false
C2R	CB	LEU- 299	4.06	0	Hydrophobic	false
N1F	N	LEU- 299	2.86	179.03	H-Bond (Protein Donor)	false
O2F	N	ASN- 300	3.05	152.52	H-Bond (Protein Donor)	false
OF2	O	HOH- 503	2.84	180	H-Bond (Protein Donor)	false
N1	O	HOH- 517	3	154.03	H-Bond (Protein Donor)	false
OA1	O	HOH- 519	2.77	151.36	H-Bond (Protein Donor)	false
OA2	O	HOH- 536	2.95	179.98	H-Bond (Protein Donor)	false
OF1	O	HOH- 544	2.84	173.01	H-Bond (Protein Donor)	false