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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4eepFMNPhototropin-22.7.11.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4eepFMNPhototropin-22.7.11.11.000
5efwFMNNPH1-1/0.586
5djtFMNNPH1-2/0.569
1g28FMNPHY3/0.566
4eetFMNPhototropin-22.7.11.10.563
5dkkFMNPredicted protein/0.548
1n9nFMNPutative blue light receptor/0.541
4hhdFMNPhototropin-12.7.11.10.541
4hj6FMNLOV protein/0.532
3ue6FMNAureochrome1/0.529
2v1aFMNNPH1-1/0.527
2z6dFMNPhototropin-22.7.11.10.526
2v0uFMNNPH1-1/0.525
4eerFMNPhototropin-22.7.11.10.523
2z6cFMNPhototropin-12.7.11.10.521
4eesFMNPhototropin-22.7.11.10.521
4r38RBFBlue-light-activated histidine kinase 22.7.13.30.519
4kukRBFPutative blue-light photoreceptor/0.513
4kuoRBFPutative blue-light photoreceptor/0.506
2pd8FADVivid PAS protein VVD/0.505
4hiaFMNLOV protein/0.498
3t50FMNBlue-light-activated histidine kinase2.7.13.30.496
3is2FADVivid PAS protein VVD/0.488
3sw1FMNSensory box protein/0.486
2pr5FMNBlue-light photoreceptor/0.485
2bxqIMNSerum albumin/0.482
2owuSAHDiphthine synthase/0.476
3p7nFMNLight-activated DNA-binding protein EL222/0.473
4hj4FMNLOV protein/0.471
2ed5SAHDiphthine synthase/0.469
1me6IVSPlasmepsin-23.4.23.390.468
4oztP1AEcdysone receptor, putative/0.468
4ih71ERGenome polyprotein2.7.7.480.467
5dp2NAPCurF/0.467
2ejzSAHDiphthine synthase/0.466
3e51N35Genome polyprotein2.7.7.480.466
1g1aNADdTDP-glucose 4,6-dehydratase/0.465
2ea2F77Methionine aminopeptidase 2/0.465
2g8yNADHydroxycarboxylate dehydrogenase B/0.465
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
2ejkSAHDiphthine synthase/0.462
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.461
3b9lAZZSerum albumin/0.460
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.459
4kwhNAPReductase homolog/0.459
3b70NAPEnoyl reductase LovC10.457
4dptAGSMevalonate diphosphate decarboxylase/0.457
4dxd9PCCell division protein FtsZ/0.457
3vw7VPXProteinase-activated receptor 1/0.457
1bsvNDPGDP-L-fucose synthase/0.456
1n9lFMNPutative blue light receptor/0.455
4j0v1H7Beta-secretase 13.4.23.460.455
1pdhFASp-hydroxybenzoate hydroxylase/0.454
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.454
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.454
4gt8ADPSensor protein VraS2.7.13.30.454
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.454
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.453
2vd0D27Hematopoietic prostaglandin D synthase/0.453
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.453
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.453
2el0SAHDiphthine synthase/0.452
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.452
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
2dv4SAHDiphthine synthase/0.451
2z6rSAHDiphthine synthase/0.451
2emuSAHDiphthine synthase/0.449
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.449
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4eeuFMNPhototropin-22.7.11.10.449
2ci01CMLanosterol 14-alpha demethylase1.14.13.700.448
2ed3SAHDiphthine synthase/0.448
2owfSAHDiphthine synthase/0.448
2p5fSAHDiphthine synthase/0.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4dfg0JVGag-Pol polyprotein3.4.23.160.448
4k6fNAPPutative Acetoacetyl-CoA reductase/0.448
1lbcCYZGlutamate receptor 2/0.447
2hutSAHDiphthine synthase/0.447
2op18PCEnoyl-ACP reductase/0.447
3i0pNADMalate dehydrogenase, putative/0.447
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.447
1diuBDMDihydrofolate reductase1.5.1.30.446
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.446
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
2e8hSAHDiphthine synthase/0.446
2ek3SAHDiphthine synthase/0.446
2pb6SAHDiphthine synthase/0.446
2pd7FADVivid PAS protein VVD/0.446
3gfbNADL-threonine 3-dehydrogenase/0.446
1wngSAHDiphthine synthase/0.445
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.445
2ek2SAHDiphthine synthase/0.445
3vmmP0DAlanine--anticapsin ligase/0.445
3zv64HBCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.445
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.445
4bfuZVUPantothenate kinase2.7.1.330.445
4s1hADPPyridoxal kinase, putative/0.445
1drhNAPDihydrofolate reductase1.5.1.30.444
1hfqMOTDihydrofolate reductase1.5.1.30.444
1udaUFGUDP-glucose 4-epimerase5.1.3.20.444
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3h06VBPGlutamate receptor 2/0.444
3hjiFADVivid PAS protein VVD/0.444
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.444
3wqmB29Diterpene synthase3.1.7.80.444
4c3yFAD3-ketosteroid dehydrogenase/0.444
4du82P0Mevalonate diphosphate decarboxylase/0.444
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.444
4prxADPDNA gyrase subunit B/0.444
5jlaNADPutative short-chain dehydrogenase/reductase/0.444
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.443
1h74ADPHomoserine kinase2.7.1.390.443
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.443
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.443
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.442
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.442
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.442
4gxs0YSGlutamate receptor 2/0.442
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.441
3qsaTA7Anthranilate phosphoribosyltransferase/0.441
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.441
4ienCOAPutative acyl-CoA hydrolase/0.441
4lb2DM5Serum albumin/0.441
4r1lADPPhenylacetate-coenzyme A ligase/0.441
1dr2TAPDihydrofolate reductase1.5.1.30.440
1gc5ADPADP-dependent glucokinase2.7.1.1470.440
1vceSAHDiphthine synthase/0.440
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.440
2givACOHistone acetyltransferase KAT8/0.440
2vojNADAlanine dehydrogenase1.4.1.10.440
2xvw9NRSerum albumin/0.440
2z4sADPChromosomal replication initiator protein DnaA/0.440
3bbpGTPRas-related protein Rab-6A/0.440
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3lqfNADGalactitol dehydrogenase/0.440
3tneRITCandidapepsin-13.4.23.240.440
4ejh0QACytochrome P450 2A131.14.14.10.440