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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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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
4kigENOPhenylpyruvate C(3)-methyltransferase2.1.1.281

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4kigENOPhenylpyruvate C(3)-methyltransferase2.1.1.2811.000
4kc2WS2Histo-blood group ABO system transferase/0.499
2zcqB65Dehydrosqualene synthase/0.485
4f6vZYMDehydrosqualene synthase/0.485
3qttANPPantothenate synthetase/0.483
3ba6AN2Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.479
3b9lAZZSerum albumin/0.477
4xzmNAPAldo-keto reductase family 1 member B101.1.10.475
1bzsBSINeutrophil collagenase3.4.24.340.474
2o6hINI6,7-dimethyl-8-ribityllumazine synthase 12.5.1.780.473
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.471
2y4kGDPUncharacterized protein/0.469
4ea0651Dehydrosqualene synthase/0.468
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.467
2vi5Y196,7-dimethyl-8-ribityllumazine synthase2.5.1.780.466
3tfp03LDehydrosqualene synthase/0.466
4jhz1KVBeta-glucuronidase3.2.1.310.466
4ddhMS0Pantothenate synthetase6.3.2.10.465
4wctFADFructosyl amine:oxygen oxidoreductase/0.465
2pauD5M5'-deoxynucleotidase YfbR/0.464
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.464
3eblGA4Gibberellin receptor GID1/0.464
3v0o4GWHisto-blood group ABO system transferase/0.463
4jxzATPGlutamine--tRNA ligase6.1.1.180.463
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.463
5ewjQELNMDA glutamate receptor subunit/0.463
5ewjQELGlutamate receptor ionotropic, NMDA 2B/0.463
2c92TP66,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
3nlvH4BNitric oxide synthase, brain1.14.13.390.461
4jyzATPGlutamine--tRNA ligase6.1.1.180.461
3v4tUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.460
4auxXTCTetracycline repressor protein class D/0.460
4cnzADPNitrogen regulatory protein P-II 1/0.460
4kc4WS3Histo-blood group ABO system transferase/0.460
2ylxNAPPhenylacetone monooxygenase1.14.13.920.459
2p1oNLAProtein TRANSPORT INHIBITOR RESPONSE 1/0.458
3rmwUPGGlycogenin-12.4.1.1860.458
2ylwNAPPhenylacetone monooxygenase1.14.13.920.457
1jstATPCyclin-dependent kinase 22.7.11.220.456
3c9sACPThiamine-monophosphate kinase/0.456
3vmmP0DAlanine--anticapsin ligase/0.456
4bzbDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.456
4d04NAPPhenylacetone monooxygenase1.14.13.920.456
1touB1VFatty acid-binding protein, adipocyte/0.455
2oyeIM8Prostaglandin G/H synthase 11.14.99.10.455
4a4zANPAntiviral helicase SKI23.6.4.130.455
5ansRX87,8-dihydro-8-oxoguanine triphosphatase3.6.1.550.455
1qrtATPGlutamine--tRNA ligase6.1.1.180.454
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.454
3c9rATPThiamine-monophosphate kinase/0.454
4gncASORegucalcin3.1.1.170.454
5ftcADPTPR domain protein/0.454
2isjFMN5,6-dimethylbenzimidazole synthase1.13.11.790.453
3fr5I4AFatty acid-binding protein, adipocyte/0.453
1p4aPCPPur operon repressor/0.452
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.452
2c2aADPSensor histidine kinase/0.452
3n10CMPAdenylate cyclase 2/0.452
3wecAUICytochrome P450/0.452
4a6nFADTetX family tetracycline inactivation enzyme/0.452
3qiyQI1Botulinum neurotoxin type A3.4.24.690.451
4b71DJLGenome polyprotein3.4.21.980.451
4ckcSAHmRNA-capping enzyme catalytic subunit2.1.1.560.451
4mb2ATPUncharacterized protein/0.450
1euyQSIGlutamine--tRNA ligase6.1.1.180.449
2i4n5CAProline--tRNA ligase6.1.1.150.449
2z6iFMN2-nitropropane dioxygenase/0.449
1fm1WAYCollagenase 33.4.240.448
2q7hYLYPyrrolysine--tRNA ligase/0.448
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.448
4bfyZVYPantothenate kinase2.7.1.330.448
4ix5ANPUncharacterized protein/0.448
4mvcCDCCholine-phosphate cytidylyltransferase A/0.448
1gzfNADMono-ADP-ribosyltransferase C32.4.20.447
1w19T4P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
1w29TS06,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
3h4vNAPPteridine reductase 11.5.1.330.447
3lpgZ78Beta-glucuronidase3.2.1.310.447
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.447
4lfgIPEPutative geranyltranstransferase/0.447
4uz6SCRPalmitoleoyl-protein carboxylesterase NOTUM/0.447
1a71NADAlcohol dehydrogenase E chain1.1.1.10.446
1hqtNAPAlcohol dehydrogenase [NADP(+)]1.1.1.20.446
1t2aGDPGDP-mannose 4,6 dehydratase4.2.1.470.446
2bxoOPBSerum albumin/0.446
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.446
2ow9SP6Collagenase 33.4.240.446
3hggCHDCmeR/0.446
3pzcCOAAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.446
3v0p4GWHisto-blood group ABO system transferase/0.446
3x22FMNOxygen-insensitive NAD(P)H nitroreductase/0.446
4eiqKCTPutative FAD-monooxygenase/0.446
4i5vB4PDiadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2/0.446
4ivoACJProtoporphyrinogen oxidase1.3.3.40.446
5fkoTDCTetracycline repressor protein class D/0.446
1g93UPGN-acetyllactosaminide alpha-1,3-galactosyltransferase/0.445
1n2gAPCPantothenate synthetase6.3.2.10.445
1wpgADPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.445
2vkuDBELanosterol 14-alpha demethylase1.14.13.700.445
3lgxATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.445
3p9uFADTetX family tetracycline inactivation enzyme/0.445
4ffrATPUncharacterized protein/0.445
4iakADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.445
5dstSAHProtein arginine N-methyltransferase 82.1.10.445
1k5dGNPGTP-binding nuclear protein Ran/0.444
1uscFMNMonooxygenase/0.444
1zotEMABifunctional hemolysin/adenylate cyclase4.6.1.10.444
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.444
3n2eOSAShikimate kinase2.7.1.710.444
4f6w0SSCyclin-dependent kinase 82.7.11.220.444
4h2uATPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.444
4hn1TYDdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.444
5f54TMPSingle-stranded-DNA-specific exonuclease/0.444
1fduNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1in5ADPHolliday junction ATP-dependent DNA helicase RuvB/0.443
1ooqFMNOxygen-insensitive NAD(P)H nitroreductase/0.443
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.10.443
2xs3ALA_PHE_THR_SERKarilysin3.4.240.443
3cehAVEGlycogen phosphorylase, liver form2.4.1.10.443
3cr7PPSAdenylyl-sulfate kinase2.7.1.250.443
4ea13RXDehydrosqualene synthase/0.443
2vprTDCTetracycline repressor protein class H/0.442
3keuATPPyridoxal kinase2.7.1.350.442
3kt3TYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.442
3orpAGSSerine/threonine protein kinase/0.442
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
1l8qADPChromosomal replication initiator protein DnaA/0.441
2rggGNPGTPase HRas/0.441
2zsbADPPantothenate kinase2.7.1.330.441
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.441
3i12ADPD-alanine--D-alanine ligase A6.3.2.40.441
3qemQEMGlutamate receptor ionotropic, NMDA 2B/0.441
3qemQEMNMDA glutamate receptor subunit/0.441
4eooATPCyclin-dependent kinase 22.7.11.220.441
4fvqATPTyrosine-protein kinase JAK2/0.441
4ii5ADPCyclin-dependent kinase 22.7.11.220.441
4xba5GPAprataxin-like protein30.441
1icvFMNOxygen-insensitive NAD(P)H nitroreductase/0.440
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1rywEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
2x3jATPAcsD/0.440
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
3cw901A4-chlorobenzoyl CoA ligase/0.440
3dntATPSerine/threonine-protein kinase toxin HipA/0.440
3o7lANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
4cthRDFNeprilysin/0.440
4fvzH4BNitric oxide synthase, brain1.14.13.390.440
4qnuGEKtRNA U34 carboxymethyltransferase/0.440