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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
1g6o ADP Cag alpha

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1g6o ADPCag alpha / 0.819
4jsy GTPMetallophosphoesterase / 0.745
1gy3 ATPCyclin-dependent kinase 2 2.7.11.22 0.744
1hk4 T44Serum albumin / 0.744
1kzj CB3Thymidylate synthase / 0.744
1sn5 T3Transthyretin / 0.744
1vrq FONSubunit alpha of sarocosine oxidase / 0.744
2pc4 ASP_TRP_ASNFructose-bisphosphate aldolase 4.1.2.13 0.744
2tsc CB3Thymidylate synthase / 0.744
3cz0 9ODPheromone-binding protein ASP1 / 0.744
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 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
4b6u M7GEukaryotic translation initiation factor 4E type 3 / 0.744
4c1f X8ZMetallo-beta-lactamase type 2 / 0.744
4dsb A8SAbscisic acid receptor PYL3 / 0.744
4ivo ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4ne0 ZZUHydroxylase / 0.744
5dby DIFSerum albumin / 0.744
5jqb IBPEnvelope glycoprotein / 0.744
3r9i ADPSeptum site-determining protein MinD / 0.740
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.739
1z0d GDPRas-related protein Rab-5C / 0.738
4gp6 ADPMetallophosphoesterase / 0.737
5fl3 ADPPili retraction protein PilT / 0.736
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.735
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.732
4ihq ADPConserved Archaeal protein / 0.731
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.730
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.730
4o2r GDPGTP-binding protein Rheb / 0.730
2o8b ADPDNA mismatch repair protein Msh2 / 0.729
2qen ADPWalker-Type ATPase / 0.729
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.729
5ftc ADPTPR domain protein / 0.729
5ftf ADPTPR domain protein / 0.729
1d5c GDPGTPase (Rab6) / 0.728
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.728
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
1wbb ADPDNA mismatch repair protein MutS / 0.728
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.728
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.727
2fna ADPUncharacterized protein / 0.726
1rrg GDPADP-ribosylation factor 1 / 0.725
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.725
1z2a GDPRas-related protein Rab-23 / 0.725
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.725
4o2l GTPGTP-binding protein Rheb / 0.725
2fe4 GDPRas-related protein Rab-6B / 0.724
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.723
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.723
4y0v GDPADP-ribosylation factor 1, putative / 0.723
4ylg GDPADP-ribosylation factor 1, putative / 0.723
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.722
3vhx GTPADP-ribosylation factor 6 / 0.721
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.720
1sdm ADPKinesin heavy chain-like protein / 0.719
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.718
3ieu GDPGTPase Era / 0.718
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.718
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.717
2y65 ADPKinesin heavy chain / 0.717
3tqc ADPPantothenate kinase / 0.716
1w5s ADPORC1-type DNA replication protein 2 / 0.714
1w5t ANPORC1-type DNA replication protein 2 / 0.714
4a51 ADPKinesin-like protein KIF11 / 0.713
4itr GDPCell division control protein 42 homolog / 0.713
4l8g GDPGTPase KRas / 0.713
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.712
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.711
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
3kkq GDPRas-related protein M-Ras / 0.711
4jl5 ADPAdenylate kinase / 0.711
4l9s GDPGTPase HRas / 0.711
4pjj ADPUnconventional myosin-VI / 0.711
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.710
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
1z6t ADPApoptotic protease-activating factor 1 / 0.710
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.710
3cob ADPKinesin heavy chain-like protein / 0.710
4epw GDPGTPase KRas / 0.710
4obe GDPGTPase KRas / 0.710
2ce2 GDPGTPase HRas / 0.709
3l9h ADPKinesin-like protein KIF11 / 0.709
4pjk ADPMyosin-2 heavy chain / 0.709
5cyo GDPSeptin-9 / 0.709
4lv6 GDPGTPase KRas / 0.708
4q02 GDPGTPase KRas / 0.708
1mma ADPMyosin-2 heavy chain / 0.707
1x1r GDPRas-related protein M-Ras / 0.707
1z0f GDPRas-related protein Rab-14 / 0.707
2zrj AGSProtein RecA / 0.707
3cph GDPRas-related protein SEC4 / 0.707
3kuc GDPRas-related protein Rap-1A / 0.707
3t1t GDPProbable gliding protein mglA / 0.707
3x1w GDPRas-related protein Rap-1b / 0.707
4epx GDPGTPase KRas / 0.707
4lpk GDPGTPase KRas / 0.707
1g16 GDPRas-related protein SEC4 / 0.706
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.706
1jx2 ADPMyosin-2 heavy chain / 0.706
1z0a GDPRas-related protein Rab-2A / 0.706
4lrw GDPGTPase KRas / 0.706
4tq9 GDPGTPase KRas / 0.706
4wa7 GDPGTPase KRas / 0.706
2bbw GP5Adenylate kinase 4, mitochondrial / 0.705
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.705
4qos ADPPsp operon transcriptional activator / 0.705
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.704
4asu ADPATP synthase subunit alpha, mitochondrial / 0.704
4dsu GDPGTPase KRas / 0.704
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.703
4g01 GDPRas-related protein RABF2b / 0.703
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.703
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.702
1fnn ADPORC1-type DNA replication protein / 0.701
4dzz ADPPlasmid partitioning protein ParF / 0.701
1ow3 GDPTransforming protein RhoA / 0.699
4cf7 ADPAdenylate kinase / 0.698
2x7e ADPKinesin-like protein KIF11 / 0.697
1sq5 ADPPantothenate kinase 2.7.1.33 0.696
1w5t ADPORC1-type DNA replication protein 2 / 0.696
2gm1 ADPKinesin-like protein KIF11 / 0.696
2pg2 ADPKinesin-like protein KIF11 / 0.696
2x2r ADPKinesin-like protein KIF11 / 0.696
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.696
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.696
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.695
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
2zfi ADPKinesin-like protein KIF1A / 0.695
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.695
4jl6 ADPAdenylate kinase / 0.694
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.694
2zro ADPProtein RecA / 0.693
2dr3 ADPUPF0273 protein PH0284 / 0.692
4jjz ADPFormate--tetrahydrofolate ligase / 0.692
4luc GDPGTPase KRas / 0.692
1yra GDPGPN-loop GTPase PAB0955 / 0.691
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.691
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
4hi0 GDPUrease accessory protein UreG / 0.691
5aun ADPIron-sulfur cluster carrier protein / 0.691
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.690
1yzq GNPRas-related protein Rab-6A / 0.690
3ea5 GDPGTP-binding nuclear protein Ran / 0.690
4o25 GTPGTP-binding protein Rheb / 0.690
5di3 GNPADP-ribosylation factor-like protein 3 / 0.690
1ky2 GNPGTP-binding protein YPT7 / 0.689
2eck ADPAdenylate kinase / 0.689
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.689
3kud GDPGTPase HRas / 0.689
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.689
4iei ADPGene 2 protein / 0.689
4kvg GTPRas-related protein Rap-1A / 0.689
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.688
1n6l GTPRas-related protein Rab-5A / 0.688
3oes GNPGTPase RhebL1 / 0.688
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.688
4goj GNPADP-ribosylation factor-like protein 3 / 0.688
4hse ADPChaperone protein ClpB / 0.688
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.688
1xtr GNPGTP-binding protein Rheb / 0.687
3zia ATPATP synthase subunit alpha, mitochondrial / 0.687
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.687
2c9o ADPRuvB-like 1 3.6.4.12 0.686
2dpx GDPGTP-binding protein RAD / 0.686
3tjz GNPADP-ribosylation factor 1 / 0.686
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.686
3rab GNPRas-related protein Rab-3A / 0.685
4qbi AP5Adenylate kinase / 0.685
1a2b GSPTransforming protein RhoA / 0.684
2whx ADPGenome polyprotein 3.4.21.91 0.684
4a1z ADPKinesin-like protein KIF11 / 0.684
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.683
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.682
4dxa GSPRas-related protein Rap-1b / 0.682
4xvq GNPGTPase HRas / 0.682
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.681
2uyi ADPKinesin-like protein KIF11 / 0.680
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.678
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.677
2ql6 ADPNicotinamide riboside kinase 1 / 0.677
3a58 GNPGTP-binding protein RHO1 / 0.677
1nbm ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
1nly AGSCag alpha / 0.676
2xsz ATPRuvB-like 2 3.6.4.12 0.676
4iok ADPFormate--tetrahydrofolate ligase / 0.676
4pfp ADPUnconventional myosin-VI / 0.675
5dha GNPGTP-binding nuclear protein Ran / 0.675
4cym GCPRas-related protein Rab-32 / 0.674
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.673
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.673
4hdq GNPRas-related protein Rap-1b / 0.673
4oi2 ADPProtein clpf-1 / 0.673
1ibr GNPGTP-binding nuclear protein Ran / 0.672
3ddc GNPGTPase HRas / 0.672
3myk ANPMyosin-2 heavy chain / 0.672
3tso GNPRas-related protein Rab-25 / 0.672
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.671
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1s1c GNPTransforming protein RhoA / 0.671
3x1z GNPRas-related protein Rap-1b / 0.671
4hdo GNPRas-related protein Rap-1b / 0.671
4jky ADPAdenylate kinase / 0.671
4ncl GDPEukaryotic translation initiation factor 5B / 0.671
5d3q GDPDynamin-1 3.6.5.5 0.671
5jlj GNPGTP-binding nuclear protein Ran / 0.671
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.670
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.670
2rgg GNPGTPase HRas / 0.670
3e5h GNPRas-related protein Rab-28 / 0.670
3i3s GNPGTPase HRas / 0.670
3k8y GNPGTPase HRas / 0.670
4zca ADPKinesin-like protein KIF11 / 0.670
1zbd GTPRas-related protein Rab-3A / 0.669
2j7p GNPSignal recognition particle protein / 0.669
2j7p GNPSignal recognition particle receptor FtsY / 0.669
2q3f GNPRas-related GTP-binding protein D / 0.669
3k9l GNPGTPase HRas / 0.669
3kko GNPRas-related protein M-Ras / 0.669
3law GNPRas-related protein Rab-7a / 0.669
3pcr GTPADP-ribosylation factor 6 / 0.669
3rs5 GNPGTPase HRas / 0.669
3tgp GNPGTPase HRas / 0.669
3v4f GNPGTPase HRas / 0.669
4dls GNPGTPase HRas / 0.669
4lhw GNPRas-related protein Rab-8A / 0.669
4dlx GNPGTPase HRas / 0.668
1z2c GNPRho-related GTP-binding protein RhoC / 0.667
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.666
3q9l ATPSeptum site-determining protein MinD / 0.665
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.665
4ap0 ADPKinesin-like protein KIF11 / 0.665
1am4 GNPCell division control protein 42 homolog / 0.664
2fg5 GNPRas-related protein Rab-31 / 0.664
3r9x GNPGTPase Era / 0.664
4idn GNPAtlastin-1 3.6.5 0.663
1a4r GNHCell division control protein 42 homolog / 0.661
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
3l1c ADPProtein claret segregational / 0.661
1diu BDMDihydrofolate reductase 1.5.1.3 0.660
1juj LYAThymidylate synthase 2.1.1.45 0.660
1oix GDPRas-related protein Rab-11A / 0.660
1rml NTSFibroblast growth factor 1 / 0.660
2hld ANPATP synthase subunit alpha, mitochondrial / 0.660
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
2qd3 CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
4ike ADPAdenylate kinase / 0.660
4jld ADPAdenylate kinase / 0.660
3uk6 ADPRuvB-like 2 3.6.4.12 0.659
4qbh AP5Adenylate kinase / 0.659
1ii6 ADPKinesin-like protein KIF11 / 0.657
4i1v ADPDephospho-CoA kinase / 0.657
4nyj GNPGTPase HRas / 0.657
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.657
2iut AGSDNA translocase FtsK / 0.656
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.656
3tlx ADPAdenylate kinase 2 / 0.655
4idp GNPAtlastin-1 3.6.5 0.655
4uj3 GNPRas-related protein Rab-11A / 0.655
4js0 GNPCell division control protein 42 homolog / 0.654
1f5n GNPGuanylate-binding protein 1 / 0.653
1lfd GNPGTPase HRas / 0.653
1uad GNPRas-related protein Ral-A / 0.653
1yu9 GNPRas-related protein Rab-4A / 0.653
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.653
3qbv GDPCell division control protein 42 homolog / 0.653
3lbn GNPGTPase HRas / 0.652
3oee ANPATP synthase subunit alpha, mitochondrial / 0.652
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.651
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.651
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
4ohx ADPProtein clpf-1 / 0.651
5bn3 ADPV-type ATP synthase alpha chain / 0.650
5bn3 ADPNEQ263 / 0.650
5k5z ANPUncharacterized protein / 0.650