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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
3gcm5GPPolyribonucleotide nucleotidyltransferase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3gcm5GPPolyribonucleotide nucleotidyltransferase/1.000
1m9k7NINitric oxide synthase, endothelial1.14.13.390.492
1b2lNDCAlcohol dehydrogenase1.1.1.10.491
3n0hTOPDihydrofolate reductase1.5.1.30.479
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.477
4bfxZVXPantothenate kinase2.7.1.330.473
4i1nFOLDihydrofolate reductase1.5.1.30.473
2rlcCHDCholoylglycine hydrolase3.5.1.240.472
3fhxPLPPyridoxal kinase2.7.1.350.472
1obnASVIsopenicillin N synthase1.21.3.10.470
1rf7DHFDihydrofolate reductase1.5.1.30.469
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.469
1m9tINENitric oxide synthase, inducible1.14.13.390.466
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.465
1fw0KAIGlutamate receptor 2/0.463
4egnTWOCytochrome P450/0.463
4bfuZVUPantothenate kinase2.7.1.330.462
2vetUMPThymidylate synthase/0.461
4yfy1YJVioF/0.461
3k8q22APurine nucleoside phosphorylase2.4.2.10.460
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2fznFADBifunctional protein PutA1.5.5.20.459
3dhk23UProthrombin3.4.21.50.459
5a0112VO-glycosyltransferase/0.459
2on6IMHPurine nucleoside phosphorylase2.4.2.10.458
4uqsINENitric oxide synthase oxygenase1.14.13.1650.458
1oc1ASVIsopenicillin N synthase1.21.3.10.457
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.457
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.456
4b1rITCTetracycline repressor protein class D/0.456
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.455
2e8hSAHDiphthine synthase/0.455
2y37A54Nitric oxide synthase, inducible1.14.13.390.455
2y6fM9FIsopenicillin N synthase1.21.3.10.455
3junAJDPhenazine biosynthesis protein A/B/0.455
4bmpFMNProtein NrdI/0.455
1towCRZFatty acid-binding protein, adipocyte/0.454
2h2jSFGRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.454
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.454
4bekXK0Beta-secretase 13.4.23.460.454
3q9bB3NAcetylpolyamine amidohydrolase/0.453
1cjuFOKAdenylate cyclase type 2/0.452
1cjuFOKAdenylate cyclase type 5/0.452
1rzuADPGlycogen synthase 12.4.1.210.452
2jh0701Prothrombin3.4.21.50.452
2zc922UProthrombin3.4.21.50.452
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.452
1vrwNAIEnoyl-ACP reductase/0.451
2zgb21UProthrombin3.4.21.50.451
2anmCDOProthrombin3.4.21.50.450
3junAKDPhenazine biosynthesis protein A/B/0.450
3s3vTOPDihydrofolate reductase1.5.1.30.450
1d6w00RProthrombin3.4.21.50.449
1s3uTQDDihydrofolate reductase1.5.1.30.449
1t4v14AProthrombin3.4.21.50.449
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.449
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.449
3p0fBAUUridine phosphorylase 22.4.2.30.449
1c4vIH2Prothrombin3.4.21.50.448
1hfqMOTDihydrofolate reductase1.5.1.30.448
1ja1FMNNADPH--cytochrome P450 reductase/0.448
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.448
3fp0FP015-O-acetyltransferase/0.448
1pl6572Sorbitol dehydrogenase1.1.1.140.447
3fr5I4AFatty acid-binding protein, adipocyte/0.447
3zw9T1GPeroxisomal bifunctional enzyme1.1.1.350.447
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.446
1dgmADNAdenosine kinase2.7.1.200.446
1nm6L86Prothrombin3.4.21.50.446
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.446
1ta6177Prothrombin3.4.21.50.446
1zgi382Prothrombin3.4.21.50.446
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.446
3ndjJHZMethyltransferase/0.446
4bfyZVYPantothenate kinase2.7.1.330.446
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.445
1qnfFADDeoxyribodipyrimidine photo-lyase4.1.99.30.445
1rszDIHPurine nucleoside phosphorylase2.4.2.10.445
1upw444Oxysterols receptor LXR-beta/0.445
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.445
2xysSY9Soluble acetylcholine receptor/0.445
4ax9N5NProthrombin3.4.21.50.445
4yfy0FXVioF/0.445
1g28FMNPHY3/0.444
1mu8CDBProthrombin3.4.21.50.444
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.444
2dhfDZFDihydrofolate reductase1.5.1.30.444
2ejzSAHDiphthine synthase/0.444
2vbpVB1Isopenicillin N synthase1.21.3.10.444
3d2mCOAAmino-acid acetyltransferase/0.444
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.444
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.444
4bamMM9Prothrombin3.4.21.50.444
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
4uy6SAHHistidine N-alpha-methyltransferase/0.444
5cc9DDFDihydrofolate reductase1.5.1.30.444
1mvsDTMDihydrofolate reductase1.5.1.30.443
3q43D66M1 family aminopeptidase3.4.110.443
4jlm1NNDeoxycytidine kinase2.7.1.740.443
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.442
1suiSAHCaffeoyl-CoA O-methyltransferase2.1.1.1040.442
1wm1PTBProline iminopeptidase3.4.11.50.442
1xddAAYIntegrin alpha-L/0.442
2jh6894Prothrombin3.4.21.50.442
2p6lSAHDiphthine synthase/0.442
3eksCY9Actin-5C/0.442
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.442
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.442
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.442
4cztCPSCBL-interacting serine/threonine-protein kinase 232.7.11.10.442
4eilUMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
4eu4COASuccinyl-CoA:acetate CoA-transferase/0.442
1culFOKAdenylate cyclase type 2/0.441
1culFOKAdenylate cyclase type 5/0.441
1d3dBZTProthrombin3.4.21.50.441
1m9m6NINitric oxide synthase, endothelial1.14.13.390.441
1pq944BOxysterols receptor LXR-beta/0.441
1zeoC01Peroxisome proliferator-activated receptor gamma/0.441
2ipjFFAAldo-keto reductase family 1 member C2/0.441
3aosJH2Hemolymph juvenile hormone binding protein/0.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3zeiAWHO-acetylserine sulfhydrylase/0.441
4bfwZVWPantothenate kinase2.7.1.330.441
4cdmFO1Deoxyribodipyrimidine photolyase/0.441
1e66HUXAcetylcholinesterase3.1.1.70.440
1t2cNAIL-lactate dehydrogenase1.1.1.270.440
1tj0FADBifunctional protein PutA1.5.5.20.440
1vceSAHDiphthine synthase/0.440
1yryMSGPurine nucleoside phosphorylase2.4.2.10.440
2e16SAHDiphthine synthase/0.440
2ea2F77Methionine aminopeptidase 2/0.440
2rqfJH3Hemolymph juvenile hormone binding protein/0.440
2zfq45UProthrombin3.4.21.50.440
2zhf49UProthrombin3.4.21.50.440
3p5pA3CTaxadiene synthase4.2.3.170.440
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
4bftZVTPantothenate kinase2.7.1.330.440
4s1iPLPPyridoxal kinase, putative/0.440
4tldAGSCircadian clock protein kinase KaiC2.7.11.10.440
4ldeP0GBeta-2 adrenergic receptor/0.440