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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
4c0b ATP mRNA cleavage and polyadenylation factor CLP1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 1.115
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.963
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.801
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.792
4qm6 GTPMetallophosphoesterase / 0.789
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.785
4ohv ANPProtein clpf-1 / 0.784
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.780
1wdt GTPElongation factor G (EF-G-2) / 0.774
3oee ANPATP synthase subunit alpha, mitochondrial / 0.769
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.769
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.768
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.767
2aky AP5Adenylate kinase / 0.765
4nh0 ATPESX secretion system protein EccC / 0.764
1esn ANPPantothenate kinase 2.7.1.33 0.763
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.761
3kko GNPRas-related protein M-Ras / 0.761
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.758
4jsy GTPMetallophosphoesterase / 0.758
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.757
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.756
4v02 ATPSite-determining protein / 0.754
4xvu ATPATPase GET3 / 0.751
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.750
1w5t ANPORC1-type DNA replication protein 2 / 0.747
3ftq GNPSeptin-2 / 0.746
1ky2 GNPGTP-binding protein YPT7 / 0.743
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.743
1zc4 GNPRas-related protein Ral-A / 0.742
1cxz GSPTransforming protein RhoA / 0.741
1n6l GTPRas-related protein Rab-5A / 0.741
3fkq ATPNtrC-like two-domain protein / 0.741
2hld ANPATP synthase subunit alpha, mitochondrial / 0.740
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.740
1gwn GTPRho-related GTP-binding protein RhoE / 0.739
3zfd ANPChromosome-associated kinesin KIF4 / 0.739
4dso GSPGTPase KRas / 0.739
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.738
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.737
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
2bc9 GNPGuanylate-binding protein 1 / 0.735
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.735
3m0e ATPTranscriptional regulator (NtrC family) / 0.735
4w5j AP5Adenylate kinase / 0.735
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.734
1f5n GNPGuanylate-binding protein 1 / 0.733
2gcp GSPRho-related GTP-binding protein RhoC / 0.732
3rs7 GNPGTPase HRas / 0.732
4qxa GTPRas-related protein Rab-9A / 0.732
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.731
3lbh GNPGTPase HRas / 0.729
3mjh GTPRas-related protein Rab-5A / 0.729
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.728
3pit GNPRas-related protein M-Ras / 0.727
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.727
5ftc ADPTPR domain protein / 0.727
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.726
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
2cl6 CAGGTPase HRas / 0.724
3a58 GNPGTP-binding protein RHO1 / 0.724
2rgc GNPGTPase HRas / 0.723
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.722
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.722
1z0d GDPRas-related protein Rab-5C / 0.722
3r9i ADPSeptum site-determining protein MinD / 0.722
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.722
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.722
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.721
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.721
1kmq GNPTransforming protein RhoA / 0.720
3oiw GNPGTPase HRas / 0.719
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.718
3rs4 GNPGTPase HRas / 0.718
3rs5 GNPGTPase HRas / 0.718
3rsl GNPGTPase HRas / 0.718
4dlt GNPGTPase HRas / 0.718
5l3s GNPSignal recognition particle receptor FtsY / 0.718
1svm ATPLarge T antigen 3.6.4 0.716
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.716
2rgg GNPGTPase HRas / 0.715
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.715
4kvg GTPRas-related protein Rap-1A / 0.715
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.714
4pjk ADPMyosin-2 heavy chain / 0.714
4pk4 ADPUnconventional myosin-VI / 0.714
1zc3 GNPRas-related protein Ral-A / 0.713
4xsg GSPTransforming protein RhoA / 0.713
2gil GTPRas-related protein Rab-6A / 0.712
3lbi GNPGTPase HRas / 0.712
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.712
2bme GNPRas-related protein Rab-4A / 0.711
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
3rs0 GNPGTPase HRas / 0.711
3v4f GNPGTPase HRas / 0.711
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.710
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.710
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.710
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
3lbn GNPGTPase HRas / 0.710
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.710
4dlw GNPGTPase HRas / 0.710
1z2a GDPRas-related protein Rab-23 / 0.709
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
4l9w GNPGTPase HRas / 0.709
4o2l GTPGTP-binding protein Rheb / 0.709
5di3 GNPADP-ribosylation factor-like protein 3 / 0.709
1d5c GDPGTPase (Rab6) / 0.708
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.708
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
2fe4 GDPRas-related protein Rab-6B / 0.707
3oes GNPGTPase RhebL1 / 0.707
4dlx GNPGTPase HRas / 0.707
4dzz ADPPlasmid partitioning protein ParF / 0.707
1fmw ATPMyosin-2 heavy chain / 0.706
2cls GTPRho-related GTP-binding protein Rho6 / 0.706
2oo7 AP5Adenylate kinase / 0.706
4dlv GNPGTPase HRas / 0.706
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.706
3k8y GNPGTPase HRas / 0.705
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.704
4js0 GNPCell division control protein 42 homolog / 0.704
4ncl GDPEukaryotic translation initiation factor 5B / 0.703
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.703
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.702
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
1m7b GTPRho-related GTP-binding protein RhoE / 0.702
1x1r GDPRas-related protein M-Ras / 0.702
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.702
2j7p GNPSignal recognition particle protein / 0.702
2j7p GNPSignal recognition particle receptor FtsY / 0.702
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.702
3tkl GTPRas-related protein Rab-1A / 0.702
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.702
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.701
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.701
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
3i3s GNPGTPase HRas / 0.701
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
4cym GCPRas-related protein Rab-32 / 0.700
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.699
2ffq GSPRas-related protein Rab-6B / 0.699
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.699
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.699
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.698
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
3oiu GNPGTPase HRas / 0.698
4ffb GTPTubulin alpha-1 chain / 0.698
4lpk GDPGTPase KRas / 0.698
1ake AP5Adenylate kinase / 0.697
2c5l GTPGTPase HRas / 0.697
2zts ADPUncharacterized protein / 0.697
3nbz GTPGTP-binding nuclear protein Ran / 0.697
4xoi GTPTransforming protein RhoA / 0.697
2fna ADPUncharacterized protein / 0.696
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.695
2x7e ADPKinesin-like protein KIF11 / 0.695
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.695
4dlz GNPGTPase HRas / 0.695
4mit GTPRho-related protein racC / 0.695
5dif GNPGTP-binding nuclear protein Ran / 0.695
1okk GCPSignal recognition particle protein / 0.694
1okk GCPSignal recognition particle receptor FtsY / 0.694
1uad GNPRas-related protein Ral-A / 0.694
2qaj AP5Adenylate kinase / 0.694
3myk ANPMyosin-2 heavy chain / 0.694
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.693
2qen ADPWalker-Type ATPase / 0.693
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.693
4idn GNPAtlastin-1 3.6.5 0.693
4o2r GDPGTP-binding protein Rheb / 0.693
2rgb GNPGTPase HRas / 0.692
3kz1 GSPTransforming protein RhoA / 0.692
4dxa GSPRas-related protein Rap-1b / 0.692
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.692
1vg8 GNPRas-related protein Rab-7a / 0.691
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
4dsn GCPGTPase KRas / 0.691
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
2o8b ADPDNA mismatch repair protein Msh2 / 0.690
4g0n GNPGTPase HRas / 0.690
4xvq GNPGTPase HRas / 0.690
1s1c GNPTransforming protein RhoA / 0.689
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.688
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.688
3zia ATPATP synthase subunit alpha, mitochondrial / 0.688
4g01 GDPRas-related protein RABF2b / 0.688
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.688
1v8k ANPKinesin-like protein KIF2C / 0.687
4iok ADPFormate--tetrahydrofolate ligase / 0.687
4lhw GNPRas-related protein Rab-8A / 0.687
1am4 GNPCell division control protein 42 homolog / 0.686
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.686
1ny5 ADPTranscriptional regulator (NtrC family) / 0.686
1rrg GDPADP-ribosylation factor 1 / 0.686
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.686
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.686
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.686
5ftf ADPTPR domain protein / 0.686
2iut AGSDNA translocase FtsK / 0.685
3oiv GNPGTPase HRas / 0.685
5aun ADPIron-sulfur cluster carrier protein / 0.685
1zbd GTPRas-related protein Rab-3A / 0.684
3kuc GDPRas-related protein Rap-1A / 0.684
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.684
1mmg AGSMyosin-2 heavy chain / 0.683
1wbb ADPDNA mismatch repair protein MutS / 0.683
2rge GNPGTPase HRas / 0.683
3ddc GNPGTPase HRas / 0.683
1xts GTPGTP-binding protein Rheb / 0.682
1g17 GNPRas-related protein SEC4 / 0.681
4nyi GNPGTPase HRas / 0.681
1sxj AGSReplication factor C subunit 1 / 0.680
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.680
4cf7 ADPAdenylate kinase / 0.680
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.680
5da9 AGSUncharacterized protein / 0.680
2osb AP5Adenylate kinase / 0.679
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.679
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.678
1oix GDPRas-related protein Rab-11A / 0.678
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.678
3k9l GNPGTPase HRas / 0.678
4rkf GNPRas-related protein Rab-3 / 0.678
4x8o AP5Adenylate kinase / 0.678
2eck ADPAdenylate kinase / 0.677
1svw GTPProbable GTP-binding protein EngB / 0.676
2r9v ATPATP synthase subunit alpha / 0.676
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
3bbp GTPRas-related protein Rab-6A / 0.675
3l8y GNPGTPase HRas / 0.675
4lja ACPChaperone protein ClpB / 0.675
4uj5 GNPRas-related protein Rab-11A / 0.675
5bn3 ADPV-type ATP synthase alpha chain / 0.675
5bn3 ADPNEQ263 / 0.675
1w5t ADPORC1-type DNA replication protein 2 / 0.674
1yu9 GNPRas-related protein Rab-4A / 0.674
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.674
3tso GNPRas-related protein Rab-25 / 0.674
4oi2 ADPProtein clpf-1 / 0.674
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.674
5hpy GDPTransforming protein RhoA / 0.674
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.673
5b2z GNPGTPase HRas / 0.673
2ce2 GDPGTPase HRas / 0.672
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.672
3rab GNPRas-related protein Rab-3A / 0.672
4ap0 ADPKinesin-like protein KIF11 / 0.672
4o25 GTPGTP-binding protein Rheb / 0.672
1z2c GNPRho-related GTP-binding protein RhoC / 0.671
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.671
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
3vhx GTPADP-ribosylation factor 6 / 0.671
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.670
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.670
2uyi ADPKinesin-like protein KIF11 / 0.670
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.670
2bku GTPGTP-binding nuclear protein Ran / 0.669
4hdo GNPRas-related protein Rap-1b / 0.669
2jlr ANPGenome polyprotein 3.4.21.91 0.668
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
3eg5 GNPCell division control protein 42 homolog / 0.668
5dha GNPGTP-binding nuclear protein Ran / 0.668
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.667
1t91 GTPRas-related protein Rab-7a / 0.667
1tu3 GNPRas-related protein Rab-5A / 0.667
1yzq GNPRas-related protein Rab-6A / 0.667
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.667
4fvq ATPTyrosine-protein kinase JAK2 / 0.667
2j5x GSPADP-ribosylation factor 6 / 0.666
3t1t GDPProbable gliding protein mglA / 0.665
4l9s GDPGTPase HRas / 0.665
4qnr ATPPsp operon transcriptional activator / 0.665
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.664
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.664
4ihq ADPConserved Archaeal protein / 0.664
4y0v GDPADP-ribosylation factor 1, putative / 0.664
4ylg GDPADP-ribosylation factor 1, putative / 0.664
5cyp GSPSeptin-9 / 0.664
3k3b ADPKinesin-like protein KIF11 / 0.663
4asu ADPATP synthase subunit alpha, mitochondrial / 0.663
4k81 GTPGTPase HRas / 0.663
4ohx ADPProtein clpf-1 / 0.663
4pfp ADPUnconventional myosin-VI / 0.663
5c46 GSPRas-related protein Rab-11A / 0.663
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.662
4uj3 GNPRas-related protein Rab-11A / 0.662
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.661
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.661
4rz3 ADPSite-determining protein / 0.661
1svl ADPLarge T antigen 3.6.4 0.660
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.660
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.659
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.659
2xtn GTPGTPase IMAP family member 2 / 0.658
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.658
3w3z GTPGTP-binding nuclear protein Ran / 0.658
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.658
4nyj GNPGTPase HRas / 0.658
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.657
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.657
4itr GDPCell division control protein 42 homolog / 0.657
1w5s ADPORC1-type DNA replication protein 2 / 0.656
2zr9 DTPProtein RecA / 0.656
3c41 ANPAmino acid ABC transporter / 0.656
4goj GNPADP-ribosylation factor-like protein 3 / 0.656
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
4mkf AP5Adenylate kinase / 0.656
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.656
1a2b GSPTransforming protein RhoA / 0.655
3rep ATPIntegrin-linked protein kinase 2.7.11.1 0.655
3tqc ADPPantothenate kinase / 0.655
5jlj GNPGTP-binding nuclear protein Ran / 0.654
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.652
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.652
3x1z GNPRas-related protein Rap-1b / 0.650
4dxj 0M9Farnesyl pyrophosphate synthase / 0.650