Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
4fjhDGTDNA-directed DNA polymerase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4fjhDGTDNA-directed DNA polymerase/1.000
4fj5DTPDNA-directed DNA polymerase/0.693
4dtoDCPDNA-directed DNA polymerase/0.635
3supDCPDNA-directed DNA polymerase/0.633
4fjlDGTDNA-directed DNA polymerase/0.633
4dtmDCPDNA-directed DNA polymerase/0.609
4fjjTTPDNA-directed DNA polymerase/0.605
4dtxTTPDNA-directed DNA polymerase/0.580
4m3tATPDNA-directed DNA polymerase/0.578
4dtpDGTDNA-directed DNA polymerase/0.577
4m42ATPDNA-directed DNA polymerase/0.547
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.524
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.514
4quvNDPDelta(14)-sterol reductase/0.511
2g96NMNNicotinamide phosphoribosyltransferase2.4.2.120.510
4m3xATPDNA-directed DNA polymerase/0.503
4rwtANPActin-5C/0.503
2qoqANPEphrin type-A receptor 32.7.10.10.502
4jlpADPAdenylate kinase/0.500
3lzjCTPDNA-directed DNA polymerase/0.499
1sesAHXSerine--tRNA ligase6.1.1.110.498
3qttANPPantothenate synthetase/0.497
4jy2FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.493
4rz3ADPSite-determining protein/0.493
1e4yAP5Adenylate kinase/0.492
2w03ADNAcsD/0.491
4dtjTTPDNA-directed DNA polymerase/0.490
3gmbFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.489
4kwwPHTNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.488
4bjzFADProbable salicylate monooxygenase/0.487
2hw1ANPKetohexokinase/0.486
2i4mPSDProline--tRNA ligase6.1.1.150.486
3c9sACPThiamine-monophosphate kinase/0.486
3hprAP5Adenylate kinase/0.486
4ckbGTPmRNA-capping enzyme catalytic subunit2.1.1.560.486
3almFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.485
2qo7ANPEphrin type-A receptor 32.7.10.10.484
3aljFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.484
1nb6UTPGenome polyprotein2.7.7.480.482
4ffrATPUncharacterized protein/0.482
1korANPArgininosuccinate synthase/0.481
2henADPEphrin type-B receptor 22.7.10.10.481
3fufBESLeukotriene A-4 hydrolase3.3.2.60.481
4h2uATPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.481
2hptBESAminopeptidase N3.4.11.20.480
2pz8APCNH(3)-dependent NAD(+) synthetase/0.480
3hv4L51Mitogen-activated protein kinase 14/0.480
4ux6H4BNitric oxide synthase, inducible1.14.13.390.480
2r59PH0Leukotriene A-4 hydrolase3.3.2.60.479
2rc3NADCBS domain/0.479
4mkhAP5Adenylate kinase/0.479
4nyeADPPhosphoribosylaminoimidazole-succinocarboxamide synthase6.3.2.60.479
3allFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.478
3ba6AN2Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.478
3fx6BPXCarboxypeptidase A13.4.17.10.478
4h2w5GPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.478
3adcANPL-seryl-tRNA(Sec) kinase2.7.1.1640.477
4fjmDCPDNA-directed DNA polymerase/0.477
4h2pFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.477
4mb2ATPUncharacterized protein/0.477
4xeoA5AAlanine--tRNA ligase, cytoplasmic/0.477
1cy7TMPDNA topoisomerase 1/0.476
2w02ATPAcsD/0.476
3gcuR48Mitogen-activated protein kinase 14/0.476
3pzcGAPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.475
4i9aNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]/0.475
5cdgNAJAlcohol dehydrogenase E chain1.1.1.10.475
2i191BYFarnesyl pyrophosphate synthase/0.474
4bw9ANPPyrrolysine--tRNA ligase/0.474
3ne6DCPDNA-directed DNA polymerase/0.473
2f94BFQFarnesyl pyrophosphate synthase2.5.1.100.472
4e6q0NVTyrosine-protein kinase JAK2/0.472
1bcpATPPertussis toxin subunit 4/0.471
1bcpATPPertussis toxin subunit 5/0.471
1n35CH1RNA-directed RNA polymerase lambda-32.7.7.480.471
2q6bHR23-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.471
5a65TPPThiamine-triphosphatase3.6.1.280.470
4gaaBESLeukotriene A(4) hydrolase/0.469
1pl2ABYGlutathione S-transferase A12.5.1.180.468
4uswATPAdenylate cyclase type 10/0.468
1fpyADPGlutamine synthetase6.3.1.20.467
1n2gAPCPantothenate synthetase6.3.2.10.466
3q9lATPSeptum site-determining protein MinD/0.466
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.465
2xkaGSPCell division protein FtsZ/0.465
4mvcCDCCholine-phosphate cytidylyltransferase A/0.465
1iinUPGGlucose-1-phosphate thymidylyltransferase2.7.7.240.464
4fk4DGTDNA-directed DNA polymerase/0.464
4k10NI9Farnesyl pyrophosphate synthase/0.464
5kj6NAJAlcohol dehydrogenase E chain1.1.1.10.464
4iazADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.463
2gvgNMNNicotinamide phosphoribosyltransferase2.4.2.120.462
1oyyAGSATP-dependent DNA helicase RecQ3.6.4.120.461
2e91ZOLGeranylgeranyl pyrophosphate synthase/0.461
3c89ARG_ARG_GLY_MET_NH2Botulinum neurotoxin type A3.4.24.690.461
4k6rATPBifunctional protein GlmU/0.461
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.460
2h3dNMNNicotinamide phosphoribosyltransferase2.4.2.120.460
5dm3ADPL-glutamine synthetase/0.460
1c0aAMOAspartate--tRNA ligase/0.459
1pf9ADP60 kDa chaperonin/0.459
1xjeGDPVitamin B12-dependent ribonucleotide reductase/0.459
1y8qATPSUMO-activating enzyme subunit 26.3.20.459
2hs0ATPPhosphoribosylformylglycinamidine synthase subunit PurL/0.459
2x0eTYDWsaF/0.459
3ftqGNPSeptin-2/0.459
3n0z3ATAdenylate cyclase 2/0.459
3ufgATPGlycine--tRNA ligase alpha subunit/0.459
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.459
1k3lGTXGlutathione S-transferase A12.5.1.180.458
1noiNTZGlycogen phosphorylase, muscle form2.4.1.10.458
2nomDUTPoly(A) polymerase, putative/0.458
2z02ATPPhosphoribosylaminoimidazole-succinocarboxamide synthase6.3.2.60.458
3e9hKAALysine--tRNA ligase6.1.1.60.458
4ez6DG3DNA polymerase I/0.458
4jxzATPGlutamine--tRNA ligase6.1.1.180.458
4lfgIPEPutative geranyltranstransferase/0.458
1g3lTRHGlucose-1-phosphate thymidylyltransferase/0.457
1px2ATPSynapsin-1/0.457
2hf8GSPProbable hydrogenase nickel incorporation protein HypB/0.457
2yqjUD1UDP-N-acetylglucosamine pyrophosphorylase2.7.7.230.457
3nwyGTPUridylate kinase/0.457
4bk2FADProbable salicylate monooxygenase/0.457
4dxhNAJAlcohol dehydrogenase E chain1.1.1.10.457
1guhGSBGlutathione S-transferase A12.5.1.180.456
1mp5UPGGlucose-1-phosphate thymidylyltransferase2.7.7.240.456
1n1dC2GGlycerol-3-phosphate cytidylyltransferase2.7.7.390.456
2iw1U2FLipopolysaccharide core biosynthesis protein RfaG2.40.456
4zo3C6LAcylhomoserine lactonase/0.456
2nadNADFormate dehydrogenase/0.455
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.455
3pzcCOAAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.455
1wc3APCAdenylate cyclase/0.454
2e8wIPEGeranylgeranyl pyrophosphate synthase/0.454
2x3fAPCPantothenate synthetase/0.454
3clrFADElectron transfer flavoprotein subunit alpha/0.454
3fwyADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein/0.454
3uwqU5POrotidine 5'-phosphate decarboxylase/0.454
4e07ACPPlasmid partitioning protein ParF/0.454
5js6NAD17-beta-hydroxysteroid dehydrogenase 141.1.10.454
4bzqADPBifunctional enzyme CysN/CysC2.7.1.250.453
4ho3TTPGlucose-1-phosphate thymidylyltransferase/0.453
4m2aUPGUDP-glucose pyrophosphorylase/0.453
4usuAPCAdenylate cyclase type 10/0.453
2jt2C90UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.452
2qa2FADPolyketide oxygenase CabE/0.452
3h5nATPMccB protein/0.452
1r0zATPCystic fibrosis transmembrane conductance regulator/0.451
2jasDTPDeoxyguanosine kinase/0.451
3gfyFMNUncharacterized protein/0.451
3keuATPPyridoxal kinase2.7.1.350.451
4dpgAPCLysine--tRNA ligase6.1.1.60.451
2vp4DCPDeoxynucleoside kinase/0.450
2x60GTPMannose-1-phosphate guanylyltransferase/0.450
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.450
5bwmNAIADP-ribosyltransferase/0.450
1khzADVADP-ribose pyrophosphatase3.6.1.130.449
1kp8AGS60 kDa chaperonin/0.449
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.449
3c4aFADProtodeoxyviolaceinate monooxygenase10.449
3zxvMXIGlutamine synthetase6.3.1.20.449
4bbe3O4Tyrosine-protein kinase JAK2/0.449
4i3p1CW3-hydroxyanthranilate 3,4-dioxygenase/0.449
4jboWPHAurora kinase A2.7.11.10.449
4qbfAP5Adenylate kinase/0.449
2q7hYLYPyrrolysine--tRNA ligase/0.448
2zs9ADPPantothenate kinase2.7.1.330.448
3nmuSAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase/0.448
3npcB96Mitogen-activated protein kinase 92.7.11.240.448
3rp8FADFAD-dependent urate hydroxylase/0.448
3u9dATPActin, alpha skeletal muscle/0.448
4kc2WS2Histo-blood group ABO system transferase/0.448
4z54GDPNeuronal-specific septin-3/0.448
1p4aPCPPur operon repressor/0.447
1wc6TATAdenylate cyclase/0.447
3ik9BOBGlutathione S-transferase A12.5.1.180.447
3q4zANPSerine/threonine-protein kinase PAK 12.7.11.10.447
4ca83ESAngiotensin-converting enzyme3.4.15.10.447
4ev0CMPCyclic AMP receptor protein/0.447
2i4n5CAProline--tRNA ligase6.1.1.150.446
3ebiBEYM1 family aminopeptidase3.4.110.446
3erkSB4Mitogen-activated protein kinase 12.7.11.240.446
3g6wGTPUracil phosphoribosyltransferase2.4.2.90.446
3ldwIPEFarnesyl pyrophosphate synthase, putative/0.446
3n0yAPCAdenylate cyclase 2/0.446
4guvFADTetX family tetracycline inactivation enzyme/0.446
4lv5ADPRhoptry protein 5B/0.446
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.445
2zsbADPPantothenate kinase2.7.1.330.445
3dj4UD1Bifunctional protein GlmU/0.445
3gueUPGUTP-glucose-1-phosphate uridylyltransferase 2, putative/0.445
3rv9RVDSalicylate synthase/0.445
4f7n0SVCyclin-dependent kinase 82.7.11.220.445
4o6mC5PUncharacterized protein/0.445
2i76NDPUncharacterized protein/0.444
2zs8ADPPantothenate kinase2.7.1.330.444
3l0hGTXGlutathione S-transferase A12.5.1.180.444
3ortAGSSerine/threonine protein kinase/0.444
3pfiADPHolliday junction ATP-dependent DNA helicase RuvB/0.444
3ryeUNRFarnesyl pyrophosphate synthase2.5.1.100.444
3w8rACPUridine kinase/0.444
4f6vZYMDehydrosqualene synthase/0.444
2uz3TTPThymidine kinase/0.443
2xdoFADTetX family tetracycline inactivation enzyme/0.443
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.443
4xjxATPType I restriction enzyme EcoR124II R protein3.1.21.30.443
1kolNADGlutathione-independent formaldehyde dehydrogenase/0.442
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.442
3c212BADNA integrity scanning protein DisA/0.442
3gegNADShort-chain dehydrogenase/reductase SDR/0.442
3nbvANPKetohexokinase/0.442
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.442
1gzfNADMono-ADP-ribosyltransferase C32.4.20.441
1u7wCTPCoenzyme A biosynthesis bifunctional protein CoaBC6.3.2.50.441
1vi2NADQuinate/shikimate dehydrogenase/0.441
2qrdADP5'-AMP-activated protein kinase subunit gamma/0.441
2r7pANPNon-structural protein 23.6.40.441
2yy5WSATryptophan--tRNA ligase6.1.1.20.441
3akyAP5Adenylate kinase/0.441
3dzdADPTranscriptional regulator (NtrC family)/0.441
3vjoANPEpidermal growth factor receptor2.7.10.10.441
4c3pACPAurora kinase A2.7.11.10.441
4fduIHSPutative multiple inositol polyphosphate histidine phosphatase 1/0.441
4khyTTPDNA-directed DNA polymerase/0.441
5c1pADPD-alanine--D-alanine ligase/0.441
5kj1NAJAlcohol dehydrogenase E chain1.1.1.10.441
1f1hADPGlutamine synthetase6.3.1.20.440
1kqnNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.440
1s3gAP5Adenylate kinase/0.440
1y56ATPUncharacterized protein/0.440
3a5yKAAElongation factor P--(R)-beta-lysine ligase/0.440
3fzfATPHeat shock cognate 71 kDa protein/0.440
3orpAGSSerine/threonine protein kinase/0.440
3zukRDFEndopeptidase, peptidase family M13/0.440
4ptfDCPDNA polymerase epsilon catalytic subunit A2.7.7.70.440
4xlvACPInsulin receptor2.7.10.10.440
4z17PEPEnolase/0.440