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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1iqr

2.100 Å

X-ray

2001-07-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Deoxyribodipyrimidine photo-lyase
ID:PHR_THET8
AC:P61497
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:4.1.99.3


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:37.253
Number of residues:48
Including
Standard Amino Acids: 48
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.3762129.625

% Hydrophobic% Polar
41.8458.16
According to VolSite

Ligand :
1iqr_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:78.38 %
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

XYZ
30.471317.430841.3883


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O2AOHTYR- 1972.65149.56H-Bond
(Protein Donor)
O1AOGSER- 2102.65165.74H-Bond
(Protein Donor)
O1ANSER- 2102.84162.03H-Bond
(Protein Donor)
O2PNARG- 2112.58152.62H-Bond
(Protein Donor)
O1PNLEU- 2123.02123.36H-Bond
(Protein Donor)
C3BCBSER- 2134.450Hydrophobic
C5'CBSER- 2133.560Hydrophobic
O1PNSER- 2133.11144.13H-Bond
(Protein Donor)
C4BCE1PHE- 2164.210Hydrophobic
C3BCD1PHE- 2164.340Hydrophobic
O1ANE1TRP- 2413.01158.41H-Bond
(Protein Donor)
C5BCE2TRP- 2413.770Hydrophobic
C1BCBGLU- 2444.450Hydrophobic
C4BCD2LEU- 2453.760Hydrophobic
O2BNH1ARG- 2482.88130.73H-Bond
(Protein Donor)
O2NH2ARG- 2483.44128.5H-Bond
(Protein Donor)
O2NH1ARG- 2482.79156.03H-Bond
(Protein Donor)
C1BCBARG- 2484.430Hydrophobic
C5'CZPHE- 3074.110Hydrophobic
C2'CBASN- 3104.350Hydrophobic
C4'CBASN- 3104.450Hydrophobic
O2'OD1ASN- 3102.73165.44H-Bond
(Ligand Donor)
C6CDARG- 3134.230Hydrophobic
C2'CDARG- 3134.50Hydrophobic
C9ACDARG- 3133.760Hydrophobic
C8CBARG- 3133.80Hydrophobic
C8MCBMET- 3143.970Hydrophobic
C7MCBALA- 3173.630Hydrophobic
C7MCE2PHE- 3354.450Hydrophobic
N3OASP- 3412.74152.43H-Bond
(Ligand Donor)
O4NASP- 3433.11161.02H-Bond
(Protein Donor)
C1'CG1VAL- 3464.130Hydrophobic
N5ND2ASN- 3472.98170.82H-Bond
(Protein Donor)
C7MCE2TRP- 3514.40Hydrophobic