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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
2uz3 TTP Thymidine kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2uz3 TTPThymidine kinase / 1.224
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.957
2wvj TTPThymidine kinase, cytosolic 2.7.1.21 0.894
2b8t THMThymidine kinase / 0.889
5fuw THMThymidine kinase, putative / 0.803
5fuv THMThymidine kinase, putative / 0.786
4uxj TTPThymidine kinase / 0.739
1v8k ANPKinesin-like protein KIF2C / 0.729
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.726
1k5d GNPGTP-binding nuclear protein Ran / 0.721
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.712
4dso GSPGTPase KRas / 0.712
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.711
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.711
3q5d GDPAtlastin-1 3.6.5 0.711
4xsg GSPTransforming protein RhoA / 0.711
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.710
4wa7 GDPGTPase KRas / 0.709
4hdq GNPRas-related protein Rap-1b / 0.708
1oix GDPRas-related protein Rab-11A / 0.706
3myk ANPMyosin-2 heavy chain / 0.703
3vhx GTPADP-ribosylation factor 6 / 0.701
2q3f GNPRas-related GTP-binding protein D / 0.699
2zrj AGSProtein RecA / 0.699
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.698
2x2r ADPKinesin-like protein KIF11 / 0.697
2xae ADPKinesin-like protein KIF11 / 0.697
3ftq GNPSeptin-2 / 0.696
4luc GDPGTPase KRas / 0.696
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.695
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
2pg2 ADPKinesin-like protein KIF11 / 0.695
2uyi ADPKinesin-like protein KIF11 / 0.695
3cob ADPKinesin heavy chain-like protein / 0.695
1a2b GSPTransforming protein RhoA / 0.694
1sdm ADPKinesin heavy chain-like protein / 0.694
2x7e ADPKinesin-like protein KIF11 / 0.694
4l8g GDPGTPase KRas / 0.694
1yrs ADPKinesin-like protein KIF11 / 0.693
2gm1 ADPKinesin-like protein KIF11 / 0.693
2y65 ADPKinesin heavy chain / 0.693
4a28 ADPKinesin-like protein KIF11 / 0.693
4lpk GDPGTPase KRas / 0.693
1ky2 GNPGTP-binding protein YPT7 / 0.692
1m7b GTPRho-related GTP-binding protein RhoE / 0.692
2zfi ADPKinesin-like protein KIF1A / 0.692
4l9s GDPGTPase HRas / 0.692
1jx2 ADPMyosin-2 heavy chain / 0.691
4ap0 ADPKinesin-like protein KIF11 / 0.691
4epw GDPGTPase KRas / 0.691
4ihq ADPConserved Archaeal protein / 0.691
4lrw GDPGTPase KRas / 0.691
4lv6 GDPGTPase KRas / 0.691
4obe GDPGTPase KRas / 0.691
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.691
5bn3 ADPV-type ATP synthase alpha chain / 0.691
5bn3 ADPNEQ263 / 0.691
2fna ADPUncharacterized protein / 0.690
2rgg GNPGTPase HRas / 0.690
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.690
3kkq GDPRas-related protein M-Ras / 0.690
3x1w GDPRas-related protein Rap-1b / 0.690
4pjj ADPUnconventional myosin-VI / 0.690
4ql3 GDPGTPase KRas / 0.690
4ww4 ADPRuvB-like helicase / 0.690
5ftc ADPTPR domain protein / 0.690
1g17 GNPRas-related protein SEC4 / 0.689
2qen ADPWalker-Type ATPase / 0.689
3cph GDPRas-related protein SEC4 / 0.689
4gp6 ADPMetallophosphoesterase / 0.689
4ldj GDPGTPase KRas / 0.689
4pfp ADPUnconventional myosin-VI / 0.689
4q03 GDPGTPase KRas / 0.689
4tq9 GDPGTPase KRas / 0.689
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.688
4asu ADPATP synthase subunit alpha, mitochondrial / 0.688
4q02 GDPGTPase KRas / 0.688
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.688
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.687
1x1r GDPRas-related protein M-Ras / 0.687
2ce2 GDPGTPase HRas / 0.687
2zts ADPUncharacterized protein / 0.687
2zxu DSTtRNA dimethylallyltransferase 2.5.1.75 0.687
4epx GDPGTPase KRas / 0.687
1mab ATPATP synthase subunit alpha, mitochondrial / 0.686
1z2a GDPRas-related protein Rab-23 / 0.686
2dpx GDPGTP-binding protein RAD / 0.686
1ow3 GDPTransforming protein RhoA / 0.685
4jjz ADPFormate--tetrahydrofolate ligase / 0.684
4pk4 ADPUnconventional myosin-VI / 0.684
4zca ADPKinesin-like protein KIF11 / 0.684
2dr3 ADPUPF0273 protein PH0284 / 0.683
2j5x GSPADP-ribosylation factor 6 / 0.682
4dzz ADPPlasmid partitioning protein ParF / 0.682
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.681
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
1rrg GDPADP-ribosylation factor 1 / 0.681
3bxz ADPProtein translocase subunit SecA / 0.681
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.681
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.681
1wbb ADPDNA mismatch repair protein MutS / 0.680
1f5n GNPGuanylate-binding protein 1 / 0.679
1nly AGSCag alpha / 0.679
2o8b ADPDNA mismatch repair protein Msh2 / 0.679
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.677
3l9h ADPKinesin-like protein KIF11 / 0.677
4dsu GDPGTPase KRas / 0.677
4ys0 ADPProtein translocase subunit SecA / 0.677
1w5s ADPORC1-type DNA replication protein 2 / 0.676
4js0 GNPCell division control protein 42 homolog / 0.676
4yqf GDPSeptin-9 / 0.676
1w5t ADPORC1-type DNA replication protein 2 / 0.675
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.675
3zia ATPATP synthase subunit alpha, mitochondrial / 0.675
4cf7 ADPAdenylate kinase / 0.675
1p72 THMThymidine kinase / 0.674
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.674
3kuc GDPRas-related protein Rap-1A / 0.674
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.674
5aun ADPIron-sulfur cluster carrier protein / 0.674
2fe4 GDPRas-related protein Rab-6B / 0.671
3k9l GNPGTPase HRas / 0.671
3zfd ANPChromosome-associated kinesin KIF4 / 0.671
4g01 GDPRas-related protein RABF2b / 0.671
1s1c GNPTransforming protein RhoA / 0.670
1svl ADPLarge T antigen 3.6.4 0.670
4xsr UPGAlr3699 protein / 0.670
4qnr ATPPsp operon transcriptional activator / 0.669
3kud GDPGTPase HRas / 0.668
3pcr GTPADP-ribosylation factor 6 / 0.668
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.668
4b7b ADPKinesin-like protein KIF11 / 0.667
4y0v GDPADP-ribosylation factor 1, putative / 0.667
4ylg GDPADP-ribosylation factor 1, putative / 0.667
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.665
2whx ADPGenome polyprotein 3.4.21.91 0.664
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.664
5di3 GNPADP-ribosylation factor-like protein 3 / 0.664
3tgp GNPGTPase HRas / 0.663
4xvq GNPGTPase HRas / 0.663
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.661
3ryk TYDdTDP-4-dehydrorhamnose 3,5-epimerase / 0.661
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.661
4o3m ADPBloom syndrome protein 3.6.4.12 0.661
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.660
2l0x GDPGTP-binding protein Rheb / 0.660
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.660
5ftf ADPTPR domain protein / 0.660
1w2g THMThymidylate kinase 2.7.4.9 0.659
2rgb GNPGTPase HRas / 0.659
4dxa GSPRas-related protein Rap-1b / 0.659
5fl3 ADPPili retraction protein PilT / 0.659
2ql6 ADPNicotinamide riboside kinase 1 / 0.658
3d8v UD1Bifunctional protein GlmU / 0.658
1sq5 ADPPantothenate kinase 2.7.1.33 0.657
2q16 ITTdITP/XTP pyrophosphatase / 0.657
3l1c ADPProtein claret segregational / 0.657
1kqm ANPMyosin heavy chain, striated muscle / 0.656
1mma ADPMyosin-2 heavy chain / 0.656
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.656
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.654
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.654
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.653
4d81 ADPAAA ATPase, central domain protein / 0.653
4ho4 THMGlucose-1-phosphate thymidylyltransferase / 0.653
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
3aez GDPPantothenate kinase 2.7.1.33 0.652
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.652
4a1z ADPKinesin-like protein KIF11 / 0.652
4itr GDPCell division control protein 42 homolog / 0.651
4jlo ADPAdenylate kinase / 0.651
4nh0 ATPESX secretion system protein EccC / 0.651
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.650
2rgc GNPGTPase HRas / 0.650
2zsa ADPPantothenate kinase 2.7.1.33 0.650
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650