Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3au2 DGT DNA polymerase beta family (X family)

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3au2 DGTDNA polymerase beta family (X family) / 0.947
4m42 ATPDNA-directed DNA polymerase / 0.778
4m3x ATPDNA-directed DNA polymerase / 0.773
4dtp DGTDNA-directed DNA polymerase / 0.765
4khy TTPDNA-directed DNA polymerase / 0.761
4dtj TTPDNA-directed DNA polymerase / 0.759
3ne6 DCPDNA-directed DNA polymerase / 0.758
4fjj TTPDNA-directed DNA polymerase / 0.758
4fj5 DTPDNA-directed DNA polymerase / 0.757
4dtx TTPDNA-directed DNA polymerase / 0.756
3lzj CTPDNA-directed DNA polymerase / 0.755
3g6x DGTDNA polymerase iota 2.7.7.7 0.750
3sup DCPDNA-directed DNA polymerase / 0.750
4fjm DCPDNA-directed DNA polymerase / 0.744
4fk4 DGTDNA-directed DNA polymerase / 0.744
4fjl DGTDNA-directed DNA polymerase / 0.743
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.743
4fjh DGTDNA-directed DNA polymerase / 0.742
4m3t ATPDNA-directed DNA polymerase / 0.738
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.724
1cjv DADAdenylate cyclase type 2 / 0.718
1cjv DADAdenylate cyclase type 5 / 0.718
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.718
4dto DCPDNA-directed DNA polymerase / 0.709
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.698
1r89 CTPCCA-adding enzyme 2.7.7.72 0.698
4dtm DCPDNA-directed DNA polymerase / 0.698
2q66 ATPPoly(A) polymerase 2.7.7.19 0.697
4u03 GTPCyclic GMP-AMP synthase / 0.689
4xj4 3ATCyclic GMP-AMP synthase / 0.682
3q23 G2PVirion DNA-directed RNA polymerase / 0.678
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.673
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.673
3hiy UTPUncharacterized protein / 0.673
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.672
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.670
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
3rbm B73Farnesyl pyrophosphate synthase, putative / 0.666
1fa0 3ATPoly(A) polymerase 2.7.7.19 0.665
4i56 1CZ3-hydroxy-3-methylglutaryl-coenzyme A reductase 1.1.1.88 0.665
4co4 ATPNitrogen regulatory protein P-II 1 / 0.664
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.663
4xul GTPUncharacterized protein mg662 / 0.663
5i4n ATPTyrosine-protein kinase JAK2 / 0.663
4xj3 GTPCyclic GMP-AMP synthase / 0.662
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.661
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.661
4i4b 1CV3-hydroxy-3-methylglutaryl-coenzyme A reductase 1.1.1.88 0.661
2ofi ADK3-methyladenine DNA glycosylase I / 0.660
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.660
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.659
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.659
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.658
3gag FMNPutative NADH dehydrogenase NAD(P)H nitroreductase / 0.658
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.657
2b51 UTPRNA editing complex protein MP57 / 0.657
3er9 3ATPoly(A) polymerase catalytic subunit 2.7.7.19 0.657
3gwf NAPCyclohexanone monooxygenase / 0.657
4idp GNPAtlastin-1 3.6.5 0.657
4mit GTPRho-related protein racC / 0.657
2plm SIB5-methylthioadenosine/S-adenosylhomocysteine deaminase 3.5.4.28 0.656
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.656
1sdw IYTPeptidyl-glycine alpha-amidating monooxygenase 1.14.17.3 0.655
1r8b ATPCCA-adding enzyme 2.7.7.72 0.654
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.654
3n8z FLPProstaglandin G/H synthase 1 1.14.99.1 0.654
4kgm ATPUncharacterized protein / 0.654
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.653
4qly FMNEnone reductase CLA-ER / 0.653
1i7c MGBS-adenosylmethionine decarboxylase proenzyme 4.1.1.50 0.652
2wow NDPTrypanothione reductase / 0.652
4gdy 0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial 2.6.1.39 0.652
4ubs DIFPentalenic acid synthase 1.14.15.11 0.652
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.652
5bur ATP2-succinylbenzoate--CoA ligase / 0.652
1vhn FMNtRNA-dihydrouridine synthase / 0.651
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.651
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.651
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.651
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.650
4nhm UN9Prolyl 3,4-dihydroxylase TPA1 1.14.11 0.650