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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3dm5 GDP Signal recognition particle 54 kDa protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dm5 GDPSignal recognition particle 54 kDa protein / 1.045
1z2a GDPRas-related protein Rab-23 / 0.752
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.744
2xf3 J01Uncharacterized protein / 0.744
3cz0 9ODPheromone-binding protein ASP1 / 0.744
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.744
3nfa CBJGag-Pol polyprotein / 0.744
3ngq 1PSCCR4-NOT transcription complex subunit 6-like 3.1.13.4 0.744
3nks ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4dsb A8SAbscisic acid receptor PYL3 / 0.744
4y0v GDPADP-ribosylation factor 1, putative / 0.744
4ylg GDPADP-ribosylation factor 1, putative / 0.744
5dby DIFSerum albumin / 0.744
5dby NPSSerum albumin / 0.744
5jqb IBPEnvelope glycoprotein / 0.744
1rrg GDPADP-ribosylation factor 1 / 0.740
3t1t GDPProbable gliding protein mglA / 0.733
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.731
1rj9 GCPSignal recognition particle receptor FtsY / 0.730
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.723
1yra GDPGPN-loop GTPase PAB0955 / 0.720
3vhx GTPADP-ribosylation factor 6 / 0.717
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.716
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.716
3ea5 GDPGTP-binding nuclear protein Ran / 0.710
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.699
3kz1 GSPTransforming protein RhoA / 0.698
5jlj GNPGTP-binding nuclear protein Ran / 0.697
2j7p GNPSignal recognition particle protein / 0.694
2j7p GNPSignal recognition particle receptor FtsY / 0.694
3r9x GNPGTPase Era / 0.694
4g01 GDPRas-related protein RABF2b / 0.692
5di3 GNPADP-ribosylation factor-like protein 3 / 0.691
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.690
4l8g GDPGTPase KRas / 0.686
4o2l GTPGTP-binding protein Rheb / 0.685
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.684
4ol0 GTPGTP-binding nuclear protein Ran / 0.684
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.683
1d5c GDPGTPase (Rab6) / 0.682
4z54 GDPNeuronal-specific septin-3 / 0.682
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.681
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.681
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.680
2q3f GNPRas-related GTP-binding protein D / 0.679
4yqf GDPSeptin-9 / 0.676
2j5x GSPADP-ribosylation factor 6 / 0.675
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.674
2bku GTPGTP-binding nuclear protein Ran / 0.674
3ieu GDPGTPase Era / 0.674
1z0d GDPRas-related protein Rab-5C / 0.672
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.668
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.667
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.667
5l3s GNPSignal recognition particle receptor FtsY / 0.667
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.664
1a2b GSPTransforming protein RhoA / 0.662
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
1rml NTSFibroblast growth factor 1 / 0.660
2qd3 CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
1wa5 GTPGTP-binding nuclear protein Ran / 0.659
1z0f GDPRas-related protein Rab-14 / 0.659
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.659
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.658
4h1v GNPDynamin-1-like protein 3.6.5.5 0.656
2xtn GTPGTPase IMAP family member 2 / 0.655
3e5h GNPRas-related protein Rab-28 / 0.654
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.652
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.652
4dso GSPGTPase KRas / 0.652
4ihq ADPConserved Archaeal protein / 0.652
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
3kkq GDPRas-related protein M-Ras / 0.651
3tjz GNPADP-ribosylation factor 1 / 0.650