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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
3jvv ACP Twitching mobility protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3jvv ACPTwitching mobility protein / 0.962
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.744
4goj GNPADP-ribosylation factor-like protein 3 / 0.726
4uj5 GNPRas-related protein Rab-11A / 0.720
5dha GNPGTP-binding nuclear protein Ran / 0.720
5k5z ANPUncharacterized protein / 0.707
1p9w ANPType II secretion system protein E / 0.706
1z0f GDPRas-related protein Rab-14 / 0.704
1z2c GNPRho-related GTP-binding protein RhoC / 0.704
1jx2 ADPMyosin-2 heavy chain / 0.702
2ffq GSPRas-related protein Rab-6B / 0.699
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.693
4qos ADPPsp operon transcriptional activator / 0.693
1e0j ANPDNA primase/helicase 2.7.7 0.692
3b1x GNPFerrous iron transport protein B / 0.692
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.692
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
1ank ANPAdenylate kinase / 0.691
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.691
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.690
2c5l GTPGTPase HRas / 0.689
3oes GNPGTPase RhebL1 / 0.689
5jlj GNPGTP-binding nuclear protein Ran / 0.687
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.686
2rgc GNPGTPase HRas / 0.686
1w5t ANPORC1-type DNA replication protein 2 / 0.685
2q3f GNPRas-related GTP-binding protein D / 0.684
1okk GCPSignal recognition particle protein / 0.683
1okk GCPSignal recognition particle receptor FtsY / 0.683
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.683
4dlz GNPGTPase HRas / 0.683
2fg5 GNPRas-related protein Rab-31 / 0.681
3k9l GNPGTPase HRas / 0.681
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.679
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1ky2 GNPGTP-binding protein YPT7 / 0.679
1n6l GTPRas-related protein Rab-5A / 0.679
3kko GNPRas-related protein M-Ras / 0.679
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.679
4cid ANPEH domain-containing protein 2 / 0.679
4idn GNPAtlastin-1 3.6.5 0.679
5dif GNPGTP-binding nuclear protein Ran / 0.679
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.678
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.678
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.678
5aun ADPIron-sulfur cluster carrier protein / 0.678
5bn3 ADPV-type ATP synthase alpha chain / 0.677
5bn3 ADPNEQ263 / 0.677
3pit GNPRas-related protein M-Ras / 0.676
3tgp GNPGTPase HRas / 0.676
4cym GCPRas-related protein Rab-32 / 0.676
4g0n GNPGTPase HRas / 0.675
1s1c GNPTransforming protein RhoA / 0.674
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.673
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.673
4itr GDPCell division control protein 42 homolog / 0.673
2rgb GNPGTPase HRas / 0.672
2rge GNPGTPase HRas / 0.672
3fkq ATPNtrC-like two-domain protein / 0.672
3r9x GNPGTPase Era / 0.672
1g17 GNPRas-related protein SEC4 / 0.670
2zet GTPRas-related protein Rab-27B / 0.669
3law GNPRas-related protein Rab-7a / 0.669
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.669
4hse ADPChaperone protein ClpB / 0.668
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.667
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
2rgg GNPGTPase HRas / 0.667
3lbh GNPGTPase HRas / 0.667
4js0 GNPCell division control protein 42 homolog / 0.667
1yu9 GNPRas-related protein Rab-4A / 0.666
2ql6 ADPNicotinamide riboside kinase 1 / 0.666
3ddc GNPGTPase HRas / 0.666
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.666
3lbn GNPGTPase HRas / 0.666
4dlt GNPGTPase HRas / 0.666
4dlv GNPGTPase HRas / 0.666
4jky ADPAdenylate kinase / 0.666
3i3s GNPGTPase HRas / 0.665
3k8y GNPGTPase HRas / 0.665
3l8y GNPGTPase HRas / 0.665
3oee ANPATP synthase subunit alpha, mitochondrial / 0.665
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3oiu GNPGTPase HRas / 0.665
3oiv GNPGTPase HRas / 0.665
3rs0 GNPGTPase HRas / 0.665
3rsl GNPGTPase HRas / 0.665
3x1z GNPRas-related protein Rap-1b / 0.665
4dls GNPGTPase HRas / 0.665
4dlw GNPGTPase HRas / 0.665
4dlx GNPGTPase HRas / 0.665
2c9o ADPRuvB-like 1 3.6.4.12 0.664
3oiw GNPGTPase HRas / 0.664
3rs4 GNPGTPase HRas / 0.664
3rs5 GNPGTPase HRas / 0.664
3rs7 GNPGTPase HRas / 0.664
3v4f GNPGTPase HRas / 0.664
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.664
5b2z GNPGTPase HRas / 0.664
1vg8 GNPRas-related protein Rab-7a / 0.663
4l9w GNPGTPase HRas / 0.663
4lhw GNPRas-related protein Rab-8A / 0.663
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.663
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.662
2bku GTPGTP-binding nuclear protein Ran / 0.662
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
4idp GNPAtlastin-1 3.6.5 0.662
4qnr ATPPsp operon transcriptional activator / 0.662
1yzq GNPRas-related protein Rab-6A / 0.661
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.661
4gp6 ADPMetallophosphoesterase / 0.661
4nyj GNPGTPase HRas / 0.661
4qm6 GTPMetallophosphoesterase / 0.661
1c3x 8IGPurine nucleoside phosphorylase 2.4.2.1 0.660
1i7c MGBS-adenosylmethionine decarboxylase proenzyme 4.1.1.50 0.660
1xms ANPProtein RecA / 0.660
2j5x GSPADP-ribosylation factor 6 / 0.660
3cph GDPRas-related protein SEC4 / 0.660
4e03 ADPPlasmid partitioning protein ParF / 0.660
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.659
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.659
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.659
1z6t ADPApoptotic protease-activating factor 1 / 0.658
2hld ANPATP synthase subunit alpha, mitochondrial / 0.658
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
3rab GNPRas-related protein Rab-3A / 0.658
3tso GNPRas-related protein Rab-25 / 0.658
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.658
4rkf GNPRas-related protein Rab-3 / 0.658
1ow3 GDPTransforming protein RhoA / 0.657
4qxa GTPRas-related protein Rab-9A / 0.657
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.656
3vhx GTPADP-ribosylation factor 6 / 0.656
4ihq ADPConserved Archaeal protein / 0.656
4jsy GTPMetallophosphoesterase / 0.656
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.656
2fe4 GDPRas-related protein Rab-6B / 0.655
4dsn GCPGTPase KRas / 0.655
4dsu GDPGTPase KRas / 0.655
1fmw ATPMyosin-2 heavy chain / 0.654
1ibr GNPGTP-binding nuclear protein Ran / 0.654
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.654
3eg5 GNPCell division control protein 42 homolog / 0.654
3lbi GNPGTPase HRas / 0.654
4jl5 ADPAdenylate kinase / 0.654
2bc9 GNPGuanylate-binding protein 1 / 0.653
3d8b ADPFidgetin-like protein 1 3.6.4 0.653
4o2l GTPGTP-binding protein Rheb / 0.653
5di3 GNPADP-ribosylation factor-like protein 3 / 0.653
1rj9 GCPSignal recognition particle receptor FtsY / 0.652
4ike ADPAdenylate kinase / 0.652
4lpk GDPGTPase KRas / 0.652
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.651
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2bme GNPRas-related protein Rab-4A / 0.651
3bc1 GNPRas-related protein Rab-27A / 0.651
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.651
3x1w GDPRas-related protein Rap-1b / 0.651
4wa7 GDPGTPase KRas / 0.651
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.651
1l8q ADPChromosomal replication initiator protein DnaA / 0.650
1tu3 GNPRas-related protein Rab-5A / 0.650
4hdo GNPRas-related protein Rap-1b / 0.650