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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
3rw9DSHSpermidine synthase2.5.1.16

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3rw9DSHSpermidine synthase2.5.1.161.000
4yv2S4MSpermidine synthase, putative/0.545
4yuzS4MSpermidine synthase, putative/0.515
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.493
3nxe2NCProtease/0.492
2dwpACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.489
1uu9BI33-phosphoinositide-dependent protein kinase 12.7.11.10.482
2d4vNADIsocitrate dehydrogenase [NADP]/0.480
3fwrADPTranscriptional repressor CcpN/0.478
2o06MTASpermidine synthase2.5.1.160.474
1p31EPUUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.473
1nzdUPGDNA beta-glucosyltransferase/0.472
2i1vADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.469
3pndFADFAD:protein FMN transferase/0.466
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.464
1hfqMOTDihydrofolate reductase1.5.1.30.463
1dg7WRBDihydrofolate reductase1.5.1.30.462
2cgu3A3Serine/threonine-protein kinase Chk12.7.11.10.462
3lzxNAPFerredoxin--NADP reductase 21.18.1.20.462
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.461
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.461
1nzfUPGDNA beta-glucosyltransferase/0.460
2uw0GVKcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.460
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.460
3qd03Q43-phosphoinositide-dependent protein kinase 12.7.11.10.459
3fwsANPTranscriptional repressor CcpN/0.458
4uyf73BBromodomain-containing protein 2/0.456
3bwcSAMSpermidine synthase, putative/0.455
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.455
1h2bNAJNAD-dependent alcohol dehydrogenase/0.454
2uxoTACHTH-type transcriptional regulator TtgR/0.454
3cgbCOACoenzyme A disulfide reductase/0.454
4ei7GDPPlasmid replication protein RepX/0.454
5cwa0GAAnthranilate synthase component 14.1.3.270.454
1j39UPGDNA beta-glucosyltransferase/0.453
2pauD5M5'-deoxynucleotidase YfbR/0.453
3oqkS52Renin3.4.23.150.453
2q7vFADThioredoxin reductase/0.452
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.452
3qcx3Q23-phosphoinositide-dependent protein kinase 12.7.11.10.452
4a99FADTetX family tetracycline inactivation enzyme/0.452
4ix6ADPUncharacterized protein/0.452
3a3bRBFLumazine protein/0.450
3bc3OPTCathepsin L13.4.22.150.450
3uyt0CKCasein kinase I isoform delta2.7.11.10.450
4ho2THMGlucose-1-phosphate thymidylyltransferase/0.450
1uvrBI83-phosphoinositide-dependent protein kinase 12.7.11.10.449
2fznFADBifunctional protein PutA1.5.5.20.449
3lshFADPyranose 2-oxidase/0.448
4dtaADNAPH(2'')-Id/0.448
1gthFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.447
2o07MTASpermidine synthase2.5.1.160.447
3k47D09Dihydrofolate reductase1.5.1.30.447
3pcrGTPADP-ribosylation factor 6/0.447
3lsiFADPyranose 2-oxidase/0.446
1fwkADPHomoserine kinase2.7.1.390.445
1xkdNAPIsocitrate dehydrogenase [NADP]/0.445
2qi6MZ8Gag-Pol polyprotein/0.445
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3k4nFADPyranose 2-oxidase/0.445
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4yuvS4MSpermidine synthase, putative/0.445
1g38NEAModification methylase TaqI2.1.1.720.444
2ejzSAHDiphthine synthase/0.444
3icrFADCoenzyme A disulfide reductase/0.444
5br7FADUDP-galactopyranose mutase/0.444
6ctsCICCitrate synthase, mitochondrial2.3.3.10.444
1dg5TOPDihydrofolate reductase1.5.1.30.443
1x1aSAMC-20 methyltransferase/0.443
2p6dSAHDiphthine synthase/0.443
2vwpNDPGlucose 1-dehydrogenase/0.443
3anxMTAPolyamine aminopropyltransferase/0.443
3h3cP1EProtein-tyrosine kinase 2-beta2.7.10.20.443
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.443
3ntaFADFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.443
4h3ySAHtRNA (guanine-N(1)-)-methyltransferase/0.443
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.443
4djhJDCKappa-type opioid receptor/0.443
1k6pXN3Gag-Pol polyprotein3.4.23.160.442
1uu3LY43-phosphoinositide-dependent protein kinase 12.7.11.10.442
1z69F425,10-methylenetetrahydromethanopterin reductase/0.442
2gcdSTUSerine/threonine-protein kinase TAO22.7.11.10.442
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.442
3fpjSAMUncharacterized protein/0.442
3fr8NDPKetol-acid reductoisomerase, chloroplastic1.1.1.860.442
3gfbNADL-threonine 3-dehydrogenase/0.442
3rasNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.442
4dbzNDPPutative ketoacyl reductase1.3.10.442
4j2wFADKynurenine 3-monooxygenase/0.442
4q72FADBifunctional protein PutA/0.442
4u03GTPCyclic GMP-AMP synthase/0.442
4xgxADPFAD:protein FMN transferase/0.442
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.441
3busSAHDemethylrebeccamycin-D-glucose O-methyltransferase/0.441
3fpzAHZThiamine thiazole synthase/0.441
4wxxSAHDNA (cytosine-5)-methyltransferase 12.1.1.370.441
1susSAHCaffeoyl-CoA O-methyltransferase2.1.1.1040.440
1u3cFADCryptochrome-1/0.440
1u3dFADCryptochrome-1/0.440
2y3sTIRTamL/0.440
3abiNADUncharacterized protein/0.440
3e2sFADBifunctional protein PutA1.5.5.20.440
3egvSAHRibosomal protein L11 methyltransferase2.1.10.440
3p67FMNPentaerythritol tetranitrate reductase/0.440
4e4m0NHTyrosine-protein kinase JAK2/0.440
4lcg1WMUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.440