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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
2bif ANP 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 1.133
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.884
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.801
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.791
4xvq GNPGTPase HRas / 0.761
3oes GNPGTPase RhebL1 / 0.760
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.758
3tnf GNPRas-related protein Rab-8A / 0.756
4idp GNPAtlastin-1 3.6.5 0.754
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.752
3tkl GTPRas-related protein Rab-1A / 0.747
4k81 GTPGTPase HRas / 0.746
1yu9 GNPRas-related protein Rab-4A / 0.744
4idn GNPAtlastin-1 3.6.5 0.742
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.742
3k9l GNPGTPase HRas / 0.739
1f5n GNPGuanylate-binding protein 1 / 0.736
1ibr GNPGTP-binding nuclear protein Ran / 0.735
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.735
4dsu GDPGTPase KRas / 0.735
4yqf GDPSeptin-9 / 0.735
1uad GNPRas-related protein Ral-A / 0.732
4hdq GNPRas-related protein Rap-1b / 0.732
3tjz GNPADP-ribosylation factor 1 / 0.731
4dvg GSPRho family GTPase / 0.731
5di3 GNPADP-ribosylation factor-like protein 3 / 0.730
3myk ANPMyosin-2 heavy chain / 0.729
3tgp GNPGTPase HRas / 0.729
4nyj GNPGTPase HRas / 0.729
4z54 GDPNeuronal-specific septin-3 / 0.729
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.728
3qbt GNPRas-related protein Rab-8A / 0.728
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.727
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.727
3bbp GTPRas-related protein Rab-6A / 0.727
1lfd GNPGTPase HRas / 0.723
2fl2 ADPKinesin-like protein KIF11 / 0.723
4uj3 GNPRas-related protein Rab-11A / 0.722
1mma ADPMyosin-2 heavy chain / 0.721
1p9w ANPType II secretion system protein E / 0.721
2bku GTPGTP-binding nuclear protein Ran / 0.721
4o2l GTPGTP-binding protein Rheb / 0.721
3ftq GNPSeptin-2 / 0.720
4lrw GDPGTPase KRas / 0.720
4a51 ADPKinesin-like protein KIF11 / 0.719
5jlj GNPGTP-binding nuclear protein Ran / 0.719
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.718
4a1z ADPKinesin-like protein KIF11 / 0.718
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.718
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.717
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.717
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
1l8q ADPChromosomal replication initiator protein DnaA / 0.717
1oix GDPRas-related protein Rab-11A / 0.717
3kko GNPRas-related protein M-Ras / 0.717
3pit GNPRas-related protein M-Ras / 0.717
4asu ADPATP synthase subunit alpha, mitochondrial / 0.717
4goj GNPADP-ribosylation factor-like protein 3 / 0.717
4tq9 GDPGTPase KRas / 0.717
1am4 GNPCell division control protein 42 homolog / 0.716
1zc4 GNPRas-related protein Ral-A / 0.716
2j5x GSPADP-ribosylation factor 6 / 0.716
4epx GDPGTPase KRas / 0.716
4wa7 GDPGTPase KRas / 0.716
1xtr GNPGTP-binding protein Rheb / 0.714
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.714
2qen ADPWalker-Type ATPase / 0.714
3zia ATPATP synthase subunit alpha, mitochondrial / 0.714
4g0n GNPGTPase HRas / 0.714
4jsy GTPMetallophosphoesterase / 0.714
2rgg GNPGTPase HRas / 0.713
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.712
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.712
1w5t ADPORC1-type DNA replication protein 2 / 0.710
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.710
2gm1 ADPKinesin-like protein KIF11 / 0.710
4lhw GNPRas-related protein Rab-8A / 0.710
4pfp ADPUnconventional myosin-VI / 0.710
4zca ADPKinesin-like protein KIF11 / 0.710
1fnn ADPORC1-type DNA replication protein / 0.709
3zfd ANPChromosome-associated kinesin KIF4 / 0.709
4dlz GNPGTPase HRas / 0.709
4pjj ADPUnconventional myosin-VI / 0.709
1jx2 ADPMyosin-2 heavy chain / 0.708
4dso GSPGTPase KRas / 0.708
4pjk ADPMyosin-2 heavy chain / 0.708
5fl3 ADPPili retraction protein PilT / 0.708
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.707
1ky2 GNPGTP-binding protein YPT7 / 0.707
3l9h ADPKinesin-like protein KIF11 / 0.707
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.707
4b7b ADPKinesin-like protein KIF11 / 0.707
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.707
5aun ADPIron-sulfur cluster carrier protein / 0.707
2pg2 ADPKinesin-like protein KIF11 / 0.706
4itr GDPCell division control protein 42 homolog / 0.706
3pcr GTPADP-ribosylation factor 6 / 0.705
3thy ADPDNA mismatch repair protein Msh2 / 0.705
1xms ANPProtein RecA / 0.704
2uyi ADPKinesin-like protein KIF11 / 0.704
2x2r ADPKinesin-like protein KIF11 / 0.704
3oee ANPATP synthase subunit alpha, mitochondrial / 0.704
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
2x7e ADPKinesin-like protein KIF11 / 0.703
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.703
5dif GNPGTP-binding nuclear protein Ran / 0.703
2ce2 GDPGTPase HRas / 0.702
3x1w GDPRas-related protein Rap-1b / 0.702
4qxa GTPRas-related protein Rab-9A / 0.702
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.702
5cyo GDPSeptin-9 / 0.702
1z0a GDPRas-related protein Rab-2A / 0.701
4xsg GSPTransforming protein RhoA / 0.701
2zr9 DTPProtein RecA / 0.700
3kud GDPGTPase HRas / 0.700
3tso GNPRas-related protein Rab-25 / 0.700
4hdo GNPRas-related protein Rap-1b / 0.700
1zc3 GNPRas-related protein Ral-A / 0.699
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.699
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.698
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.698
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
3w3z GTPGTP-binding nuclear protein Ran / 0.698
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.698
4hi0 GDPUrease accessory protein UreG / 0.697
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.696
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
3tqc ADPPantothenate kinase / 0.696
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.695
2gcp GSPRho-related GTP-binding protein RhoC / 0.695
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.695
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.695
3x1z GNPRas-related protein Rap-1b / 0.695
1n6l GTPRas-related protein Rab-5A / 0.694
2hld ANPATP synthase subunit alpha, mitochondrial / 0.694
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.694
4qbg AP5Adenylate kinase / 0.694
5dha GNPGTP-binding nuclear protein Ran / 0.694
3l8y GNPGTPase HRas / 0.693
4d81 ADPAAA ATPase, central domain protein / 0.693
4xvr GNPGTPase HRas / 0.693
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
2cl6 CAGGTPase HRas / 0.692
3oiw GNPGTPase HRas / 0.692
3v4f GNPGTPase HRas / 0.692
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.691
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.691
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.691
4jjz ADPFormate--tetrahydrofolate ligase / 0.690
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.689
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.689
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.689
4iei ADPGene 2 protein / 0.689
4l8g GDPGTPase KRas / 0.689
1a2b GSPTransforming protein RhoA / 0.688
1mmg AGSMyosin-2 heavy chain / 0.688
1w5s ADPORC1-type DNA replication protein 2 / 0.688
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.688
2zrj AGSProtein RecA / 0.688
4xvu ATPATPase GET3 / 0.688
1g16 GDPRas-related protein SEC4 / 0.687
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.687
2eck ADPAdenylate kinase / 0.687
2ql6 ADPNicotinamide riboside kinase 1 / 0.687
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.687
3k1j ADPATP-dependent protease Lon / 0.687
4ihq ADPConserved Archaeal protein / 0.686
4ncl GDPEukaryotic translation initiation factor 5B / 0.686
4o2r GDPGTP-binding protein Rheb / 0.686
1sq5 ADPPantothenate kinase 2.7.1.33 0.685
2l0x GDPGTP-binding protein Rheb / 0.685
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.684
1z0d GDPRas-related protein Rab-5C / 0.684
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.684
4ike ADPAdenylate kinase / 0.684
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.683
4dlx GNPGTPase HRas / 0.683
4epw GDPGTPase KRas / 0.683
4nh0 ATPESX secretion system protein EccC / 0.683
4obe GDPGTPase KRas / 0.683
4oi2 ADPProtein clpf-1 / 0.683
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.682
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2zfi ADPKinesin-like protein KIF1A / 0.682
3kkq GDPRas-related protein M-Ras / 0.682
1ank ANPAdenylate kinase / 0.681
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.681
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.681
1rrg GDPADP-ribosylation factor 1 / 0.681
3mjh GTPRas-related protein Rab-5A / 0.681
4ql3 GDPGTPase KRas / 0.681
1x1r GDPRas-related protein M-Ras / 0.680
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.680
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.680
4ldj GDPGTPase KRas / 0.680
4q03 GDPGTPase KRas / 0.680
1z0f GDPRas-related protein Rab-14 / 0.679
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.679
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.679
3a6p GTPGTP-binding nuclear protein Ran / 0.679
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.679
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.679
1z2a GDPRas-related protein Rab-23 / 0.678
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.678
3rs4 GNPGTPase HRas / 0.678
4l9w GNPGTPase HRas / 0.678
1vg8 GNPRas-related protein Rab-7a / 0.677
2fna ADPUncharacterized protein / 0.677
2gil GTPRas-related protein Rab-6A / 0.677
3i3s GNPGTPase HRas / 0.677
3oiv GNPGTPase HRas / 0.677
3rs5 GNPGTPase HRas / 0.677
4dls GNPGTPase HRas / 0.677
4ylg GDPADP-ribosylation factor 1, putative / 0.677
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.677
3k8y GNPGTPase HRas / 0.676
3kz1 GSPTransforming protein RhoA / 0.676
3oiu GNPGTPase HRas / 0.676
3q5d GDPAtlastin-1 3.6.5 0.676
4dlv GNPGTPase HRas / 0.676
4dlw GNPGTPase HRas / 0.676
4y0v GDPADP-ribosylation factor 1, putative / 0.676
4pk4 ADPUnconventional myosin-VI / 0.675
4qos ADPPsp operon transcriptional activator / 0.675
5b2z GNPGTPase HRas / 0.675
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.674
1wbb ADPDNA mismatch repair protein MutS / 0.673
2ncd ADPProtein claret segregational / 0.673
2q2y ADPKinesin-like protein KIF11 / 0.673
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.672
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.672
3rs0 GNPGTPase HRas / 0.672
4dlt GNPGTPase HRas / 0.672
4gp6 ADPMetallophosphoesterase / 0.672
4iok ADPFormate--tetrahydrofolate ligase / 0.672
5l3s GNPSignal recognition particle receptor FtsY / 0.672
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.671
2c9o ADPRuvB-like 1 3.6.4.12 0.671
2dr3 ADPUPF0273 protein PH0284 / 0.671
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.671
3wyf GTPGTP-binding nuclear protein / 0.671
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.671
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.670
3lbn GNPGTPase HRas / 0.670
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.669
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.669
2zts ADPUncharacterized protein / 0.669
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.669
1w5t ANPORC1-type DNA replication protein 2 / 0.668
3fkq ATPNtrC-like two-domain protein / 0.668
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.668
5ftf ADPTPR domain protein / 0.668
2fe4 GDPRas-related protein Rab-6B / 0.667
2ffq GSPRas-related protein Rab-6B / 0.667
3l1c ADPProtein claret segregational / 0.667
4c30 ANPDNA helicase / 0.667
1g6o ADPCag alpha / 0.666
4c2u ANPDNA helicase / 0.666
4ol0 GTPGTP-binding nuclear protein Ran / 0.666
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.666
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.665
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
1yra GDPGPN-loop GTPase PAB0955 / 0.665
4hse ADPChaperone protein ClpB / 0.665
1xmv ADPProtein RecA / 0.664
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.664
4nyi GNPGTPase HRas / 0.664
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
2g1q ADPKinesin-like protein KIF11 / 0.663
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.663
4ohx ADPProtein clpf-1 / 0.663
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1v8k ANPKinesin-like protein KIF2C / 0.662
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.662
2y65 ADPKinesin heavy chain / 0.662
3b1x GNPFerrous iron transport protein B / 0.662
3lbi GNPGTPase HRas / 0.662
3q9l ATPSeptum site-determining protein MinD / 0.662
4ap0 ADPKinesin-like protein KIF11 / 0.662
4luc GDPGTPase KRas / 0.662
3vhx GTPADP-ribosylation factor 6 / 0.661
2vos ADPFolylpolyglutamate synthase / 0.660
2xae ADPKinesin-like protein KIF11 / 0.660
3eg5 GNPCell division control protein 42 homolog / 0.660
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.660
3ieu GDPGTPase Era / 0.660
3lbh GNPGTPase HRas / 0.660
4dzz ADPPlasmid partitioning protein ParF / 0.660
4js0 GNPCell division control protein 42 homolog / 0.660
4lpk GDPGTPase KRas / 0.660
4ww4 ADPRuvB-like helicase / 0.660
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.659
2xsz ATPRuvB-like 2 3.6.4.12 0.659
3ea5 GDPGTP-binding nuclear protein Ran / 0.659
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.659
1d5c GDPGTPase (Rab6) / 0.658
2q3f GNPRas-related GTP-binding protein D / 0.658
4d0l GSPRas-related protein Rab-11A / 0.658
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.657
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
2rgb GNPGTPase HRas / 0.657
4cym GCPRas-related protein Rab-32 / 0.657
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.657
4rkf GNPRas-related protein Rab-3 / 0.657
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.656
2rge GNPGTPase HRas / 0.656
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.656
4jld ADPAdenylate kinase / 0.656
1a4r GNHCell division control protein 42 homolog / 0.655
2bc9 GNPGuanylate-binding protein 1 / 0.655
3c41 ANPAmino acid ABC transporter / 0.655
1nly AGSCag alpha / 0.654
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.654
4a28 ADPKinesin-like protein KIF11 / 0.654
4ohv ANPProtein clpf-1 / 0.654
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.654
2fg5 GNPRas-related protein Rab-31 / 0.653
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.653
2zro ADPProtein RecA / 0.653
4db1 ANPMyosin-7 / 0.653
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.652
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.652
1t91 GTPRas-related protein Rab-7a / 0.652
4jky ADPAdenylate kinase / 0.652
4jl5 ADPAdenylate kinase / 0.652
4jl6 ADPAdenylate kinase / 0.652
1yrs ADPKinesin-like protein KIF11 / 0.651
1yzq GNPRas-related protein Rab-6A / 0.651
2rgc GNPGTPase HRas / 0.651
3cob ADPKinesin heavy chain-like protein / 0.651
3hqd ANPKinesin-like protein KIF11 / 0.651
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.651
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.651
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
4dxa GSPRas-related protein Rap-1b / 0.651
4jlo ADPAdenylate kinase / 0.651
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.651
1z6t ADPApoptotic protease-activating factor 1 / 0.650
2c5l GTPGTPase HRas / 0.650
3rs7 GNPGTPase HRas / 0.650
3rsl GNPGTPase HRas / 0.650
3t1t GDPProbable gliding protein mglA / 0.650