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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
2vp0 TTP Deoxynucleoside kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vp0 TTPDeoxynucleoside kinase / 1.483
2jcs TTPDeoxynucleoside kinase / 1.428
1zm7 TTPDeoxynucleoside kinase / 1.387
1oe0 TTPDeoxynucleoside kinase / 1.377
2vp2 DGTDeoxynucleoside kinase / 1.188
2vp4 DCPDeoxynucleoside kinase / 1.103
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.751
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.742
4mkf AP5Adenylate kinase / 0.738
1p6x THMThymidine kinase / 0.736
1p72 THMThymidine kinase / 0.734
1ot3 THMDeoxynucleoside kinase / 0.725
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.713
1rj9 GCPSignal recognition particle receptor FtsY / 0.712
3tgp GNPGTPase HRas / 0.712
4qm6 GTPMetallophosphoesterase / 0.709
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.708
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
2rgx AP5Adenylate kinase / 0.707
1v8k ANPKinesin-like protein KIF2C / 0.702
3krf DSTGeranyl diphosphate synthase large subunit / 0.700
5fuv THMThymidine kinase, putative / 0.700
5jlj GNPGTP-binding nuclear protein Ran / 0.700
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.694
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.694
4d0l GSPRas-related protein Rab-11A / 0.693
4xsg GSPTransforming protein RhoA / 0.692
5dif GNPGTP-binding nuclear protein Ran / 0.691
4tyq AP5Adenylate kinase / 0.689
1k5d GNPGTP-binding nuclear protein Ran / 0.687
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.685
4nyi GNPGTPase HRas / 0.685
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.684
3oiu GNPGTPase HRas / 0.684
4rkf GNPRas-related protein Rab-3 / 0.684
2rgb GNPGTPase HRas / 0.683
3lbn GNPGTPase HRas / 0.683
3m0e ATPTranscriptional regulator (NtrC family) / 0.683
3x1z GNPRas-related protein Rap-1b / 0.683
4dlw GNPGTPase HRas / 0.683
4l9w GNPGTPase HRas / 0.683
2bme GNPRas-related protein Rab-4A / 0.682
3l8y GNPGTPase HRas / 0.682
3rab GNPRas-related protein Rab-3A / 0.682
5i4n ATPTyrosine-protein kinase JAK2 / 0.682
4c30 ANPDNA helicase / 0.681
4dxj 0M9Farnesyl pyrophosphate synthase / 0.680
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.679
5dha GNPGTP-binding nuclear protein Ran / 0.679
2c5l GTPGTPase HRas / 0.678
2jas DTPDeoxyguanosine kinase / 0.678
2vqs BVDDeoxynucleoside kinase / 0.678
1sdm ADPKinesin heavy chain-like protein / 0.677
3tkl GTPRas-related protein Rab-1A / 0.677
3k8y GNPGTPase HRas / 0.676
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.675
3n0z 3ATAdenylate cyclase 2 / 0.675
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.674
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.674
4xr9 TMPCalS8 / 0.674
4tnq TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.672
1wa5 GTPGTP-binding nuclear protein Ran / 0.671
4qbh AP5Adenylate kinase / 0.671
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.670
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.670
4nu0 AP5Adenylate kinase / 0.670
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.670
2c96 ATPPsp operon transcriptional activator / 0.668
2oap ANPType II secretion system protein (GspE-2) / 0.668
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.668
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.668
3oab DSTGeranyl diphosphate synthase large subunit / 0.667
4asu ADPATP synthase subunit alpha, mitochondrial / 0.667
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.666
4db1 ANPMyosin-7 / 0.666
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.666
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.665
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.664
2qaj AP5Adenylate kinase / 0.664
4mit GTPRho-related protein racC / 0.664
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
2cvw TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.663
4k81 GTPGTPase HRas / 0.663
4c2u ANPDNA helicase / 0.662
4dtj TTPDNA-directed DNA polymerase / 0.662
2osb AP5Adenylate kinase / 0.660
3ldw IPEFarnesyl pyrophosphate synthase, putative / 0.660
3ne6 DCPDNA-directed DNA polymerase / 0.660
3vth APCCarbamoyltransferase / 0.660
4pxz CLRP2Y purinoceptor 12 / 0.659
4xvr GNPGTPase HRas / 0.658
1fxo TMPGlucose-1-phosphate thymidylyltransferase / 0.657
1g0r THMGlucose-1-phosphate thymidylyltransferase / 0.657
3cob ADPKinesin heavy chain-like protein / 0.657
1wdt GTPElongation factor G (EF-G-2) / 0.656
1mab ATPATP synthase subunit alpha, mitochondrial / 0.655
1ss9 UPFLgtC / 0.655
3o3p GDDGlycosyl transferase, family 2 / 0.654
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.654
1p52 ADPArginine kinase 2.7.3.3 0.653
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.653
2dpx GDPGTP-binding protein RAD / 0.653
3dkv AP5Adenylate kinase / 0.653
3law GNPRas-related protein Rab-7a / 0.653
3rs4 GNPGTPase HRas / 0.653
3v4f GNPGTPase HRas / 0.653
4dlx GNPGTPase HRas / 0.653
4dlz GNPGTPase HRas / 0.653
4lv8 ADPRhoptry protein 5 C / 0.653
3pit GNPRas-related protein M-Ras / 0.652
4nke IPEFarnesyl pyrophosphate synthase 2.5.1.10 0.652
4ol0 GTPGTP-binding nuclear protein Ran / 0.652
1gjr NAPFerredoxin--NADP reductase 1.18.1.2 0.651
3elb C5PEthanolamine-phosphate cytidylyltransferase 2.7.7.14 0.651
4b7b ADPKinesin-like protein KIF11 / 0.651
1xqp 8HGN-glycosylase/DNA lyase / 0.650