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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
1zm7 TTP Deoxynucleoside kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1zm7 TTPDeoxynucleoside kinase / 1.475
2vp0 TTPDeoxynucleoside kinase / 1.387
2jcs TTPDeoxynucleoside kinase / 1.377
1oe0 TTPDeoxynucleoside kinase / 1.117
2vp4 DCPDeoxynucleoside kinase / 1.112
2vp2 DGTDeoxynucleoside kinase / 1.032
4qm6 GTPMetallophosphoesterase / 0.782
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.724
1p6x THMThymidine kinase / 0.723
3b1x GNPFerrous iron transport protein B / 0.720
1p72 THMThymidine kinase / 0.719
4jsy GTPMetallophosphoesterase / 0.717
2jj8 AZZDeoxynucleoside kinase / 0.715
1tu3 GNPRas-related protein Rab-5A / 0.712
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.711
1rj9 GCPSignal recognition particle receptor FtsY / 0.708
4idn GNPAtlastin-1 3.6.5 0.708
5fuv THMThymidine kinase, putative / 0.708
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.707
1f5n GNPGuanylate-binding protein 1 / 0.703
2bme GNPRas-related protein Rab-4A / 0.699
3myk ANPMyosin-2 heavy chain / 0.698
1yu9 GNPRas-related protein Rab-4A / 0.697
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.697
3m0e ATPTranscriptional regulator (NtrC family) / 0.697
4goj GNPADP-ribosylation factor-like protein 3 / 0.695
5dha GNPGTP-binding nuclear protein Ran / 0.695
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.694
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
2uyi ADPKinesin-like protein KIF11 / 0.694
1a2b GSPTransforming protein RhoA / 0.693
3ddc GNPGTPase HRas / 0.693
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.691
2jlr ANPGenome polyprotein 3.4.21.91 0.689
3w3z GTPGTP-binding nuclear protein Ran / 0.689
5fuw THMThymidine kinase, putative / 0.686
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.685
3zfd ANPChromosome-associated kinesin KIF4 / 0.684
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.682
2gcp GSPRho-related GTP-binding protein RhoC / 0.682
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.681
2bku GTPGTP-binding nuclear protein Ran / 0.680
3aky AP5Adenylate kinase / 0.680
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.680
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.678
5jlj GNPGTP-binding nuclear protein Ran / 0.678
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.677
5c46 GSPRas-related protein Rab-11A / 0.675
1ot3 THMDeoxynucleoside kinase / 0.673
2y65 ADPKinesin heavy chain / 0.673
3ahe THDProbable phosphoketolase / 0.673
4dls GNPGTPase HRas / 0.673
1fmw ATPMyosin-2 heavy chain / 0.672
1wdt GTPElongation factor G (EF-G-2) / 0.672
2vqs BVDDeoxynucleoside kinase / 0.672
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.672
4xvr GNPGTPase HRas / 0.672
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
3oiu GNPGTPase HRas / 0.671
3i3s GNPGTPase HRas / 0.670
3k8y GNPGTPase HRas / 0.670
3rs0 GNPGTPase HRas / 0.670
3rs5 GNPGTPase HRas / 0.670
3rs7 GNPGTPase HRas / 0.670
3v4f GNPGTPase HRas / 0.670
4dlw GNPGTPase HRas / 0.670
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.669
3lbi GNPGTPase HRas / 0.669
4ql3 GDPGTPase KRas / 0.669
5b2z GNPGTPase HRas / 0.669
1ky2 GNPGTP-binding protein YPT7 / 0.668
2rgg GNPGTPase HRas / 0.668
3ahi HTLProbable phosphoketolase / 0.668
4q03 GDPGTPase KRas / 0.668
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.667
3e5h GNPRas-related protein Rab-28 / 0.667
4dlv GNPGTPase HRas / 0.667
3lbn GNPGTPase HRas / 0.666
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.666
3q6j KPC2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.665
4c30 ANPDNA helicase / 0.665
4mit GTPRho-related protein racC / 0.665
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.665
5itz GTPTubulin alpha-1B chain / 0.665
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.664
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.664
4xoi GTPTransforming protein RhoA / 0.664
1n5i TMPThymidylate kinase 2.7.4.9 0.663
2ixk TDOdTDP-4-dehydrorhamnose 3,5-epimerase 5.1.3.13 0.663
3rs4 GNPGTPase HRas / 0.663
1p3j AP5Adenylate kinase / 0.662
1svm ATPLarge T antigen 3.6.4 0.662
3elb C5PEthanolamine-phosphate cytidylyltransferase 2.7.7.14 0.662
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.662
1gwn GTPRho-related GTP-binding protein RhoE / 0.661
2x7e ADPKinesin-like protein KIF11 / 0.661
3oiw GNPGTPase HRas / 0.661
4dzz ADPPlasmid partitioning protein ParF / 0.661
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.661
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
2q3f GNPRas-related GTP-binding protein D / 0.660
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.659
4m3x ATPDNA-directed DNA polymerase / 0.659
4nyj GNPGTPase HRas / 0.659
1xs4 DCPdCTP deaminase / 0.658
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.658
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.658
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.658
3ahj TPPProbable phosphoketolase / 0.657
4yai NAIC alpha-dehydrogenase / 0.657
5ify UMPGlucose-1-phosphate thymidylyltransferase / 0.657
1k5d GNPGTP-binding nuclear protein Ran / 0.656
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.656
3pcr GTPADP-ribosylation factor 6 / 0.656
3c41 ANPAmino acid ABC transporter / 0.655
1foa UD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase 2.4.1.101 0.654
2pyw ADPMethylthioribose kinase 2.7.1.100 0.654
4v02 ATPSite-determining protein / 0.654
3k9l GNPGTPase HRas / 0.651
3ncq ATPNitrogen regulatory protein P-II (GlnB-2) / 0.651
4idp GNPAtlastin-1 3.6.5 0.651
4nh0 ATPESX secretion system protein EccC / 0.651
1p7c T5AThymidine kinase / 0.650
1s1c GNPTransforming protein RhoA / 0.650
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
4ol0 GTPGTP-binding nuclear protein Ran / 0.650
5i4n ATPTyrosine-protein kinase JAK2 / 0.650