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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
5im3DTPRibonucleoside-diphosphate reductase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
5im3DTPRibonucleoside-diphosphate reductase/1.000
2wghDTPRibonucleoside-diphosphate reductase large subunit1.17.4.10.553
1xjjDGTVitamin B12-dependent ribonucleotide reductase/0.498
2cig1DGDihydrofolate reductase1.5.1.30.490
3nxxNDPDihydrofolate reductase1.5.1.30.487
1xjgDTPVitamin B12-dependent ribonucleotide reductase/0.486
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.485
1u4dDBQActivated CDC42 kinase 1/0.483
3a1nNADNDP-sugar epimerase/0.482
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.481
1dr3HBIDihydrofolate reductase1.5.1.30.478
3oibFDAPutative acyl-CoA dehydrogenase/0.477
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.476
1vyrFMNPentaerythritol tetranitrate reductase/0.475
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.474
1dr3TAPDihydrofolate reductase1.5.1.30.473
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.473
1xjeTTPVitamin B12-dependent ribonucleotide reductase/0.473
2gblATPCircadian clock protein kinase KaiC2.7.11.10.473
3nr4PYVAbscisic acid receptor PYL2/0.472
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.471
3p84FMNPentaerythritol tetranitrate reductase/0.471
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.471
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.471
3pd2A3SThreonine--tRNA ligase6.1.1.30.469
3wv7ADPHmd co-occurring protein HcgE/0.469
4gk3L87Ephrin type-A receptor 32.7.10.10.469
2zbaZBATrichothecene 3-O-acetyltransferase/0.468
3o0oTTPVitamin B12-dependent ribonucleotide reductase/0.468
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.466
1dyjDDFDihydrofolate reductase1.5.1.30.465
1v9aSAHUncharacterized protein/0.465
3ft8MOJHeat shock protein HSP 90-alpha/0.465
4eji0QACytochrome P450 2A131.14.14.10.465
5eccNAPDehydrofolate reductase type I/0.464
1u54ACPActivated CDC42 kinase 1/0.463
2fy4COACholine O-acetyltransferase2.3.1.60.463
3a4vNADNDP-sugar epimerase/0.463
4c02TAKActivin receptor type-12.7.11.300.463
4cukNAID-lactate dehydrogenase/0.463
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.463
1bsvNDPGDP-L-fucose synthase/0.462
3f03FMNPentaerythritol tetranitrate reductase/0.462
4b8wNAPGDP-L-fucose synthase1.1.1.2710.462
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.461
1m78NDPDihydrofolate reductase1.5.1.30.461
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.461
2w71L23Biotin carboxylase6.3.4.140.461
3oafOAGDihydrofolate reductase1.5.1.30.461
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
1gqtACPRibokinase/0.460
2rhrEMOPutative ketoacyl reductase1.3.10.460
3fln3FNMitogen-activated protein kinase 14/0.460
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.460
1c1dNAIPhenylalanine dehydrogenase/0.459
1jpaANPEphrin type-B receptor 22.7.10.10.459
1xjnDTPVitamin B12-dependent ribonucleotide reductase/0.459
4i8vBHFCytochrome P450 1A11.14.14.10.459
4rrrA3TThreonine--tRNA ligase6.1.1.30.459
5e8wSTUTGF-beta receptor type-12.7.11.300.459
1dr2TAPDihydrofolate reductase1.5.1.30.458
1xelUPGUDP-glucose 4-epimerase5.1.3.20.458
2r1rTTPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.458
3crzFADFerredoxin--NADP+ reductase/0.458
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.458
3uyt0CKCasein kinase I isoform delta2.7.11.10.458
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.458
1a72PADAlcohol dehydrogenase E chain1.1.1.10.457
1rx8FOLDihydrofolate reductase1.5.1.30.457
1udaUFGUDP-glucose 4-epimerase5.1.3.20.457
1yjqNAP2-dehydropantoate 2-reductase1.1.1.1690.457
3cgcCOACoenzyme A disulfide reductase/0.457
3hllI45Mitogen-activated protein kinase 14/0.457
3o0qTTPVitamin B12-dependent ribonucleotide reductase/0.457
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.457
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.457
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.457
1dhrNADDihydropteridine reductase1.5.1.340.456
1t2cNAIL-lactate dehydrogenase1.1.1.270.456
4l4xNDPAmphI/0.456
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.456
1ai9NDPDihydrofolate reductase1.5.1.30.455
1ia4TQ6Dihydrofolate reductase1.5.1.30.455
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.455
4dieC5PCytidylate kinase/0.455
4g95OAGDihydrofolate reductase1.5.1.30.455
5a3cNADSIR2 family protein/0.455
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.454
3mvm39PMitogen-activated protein kinase 14/0.454
3pd4A3GThreonine--tRNA ligase6.1.1.30.454
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.454
1nzdUPGDNA beta-glucosyltransferase/0.453
4nbwNADShort-chain dehydrogenase/reductase SDR/0.453
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.452
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.452
1h74ADPHomoserine kinase2.7.1.390.452
2a4nCOAAac(6')-Ii protein/0.452
2a94AP0L-lactate dehydrogenase1.1.1.270.452
2qo9ANPEphrin type-A receptor 32.7.10.10.452
3fwjCAMCamphor 5-monooxygenase1.14.15.10.452
3hrfATP3-phosphoinositide-dependent protein kinase 12.7.11.10.452
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4dymIYZActivin receptor type-12.7.11.300.452
1q4t4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.451
1xddAAYIntegrin alpha-L/0.451
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.451
5itzGTPTubulin alpha-1B chain/0.451
1a59COA2-methylcitrate synthase/0.450
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.450
1rfvADPPyridoxal kinase2.7.1.350.450
2fhnBNIAvidin-related protein 4/5/0.450
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.450
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
4du82P0Mevalonate diphosphate decarboxylase/0.450
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.450
1i59ANPChemotaxis protein CheA2.7.13.30.449
1tf7ATPCircadian clock protein kinase KaiC2.7.11.10.449
2xa4AZ5Tyrosine-protein kinase JAK2/0.449
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.449
3in6FMNUncharacterized protein/0.449
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.449
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3rfxNADUronate dehydrogenase/0.449
4b8zNAPGDP-L-fucose synthase1.1.1.2710.449
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.449
4mv8ACPBiotin carboxylase6.3.4.140.449
5cccDDFDihydrofolate reductase1.5.1.30.449
1ny5ADPTranscriptional regulator (NtrC family)/0.448
1pr9NAPL-xylulose reductase1.1.1.100.448
2hk9NAPShikimate dehydrogenase (NADP(+))/0.448
2q29ACOOxalyl-CoA decarboxylase4.1.1.80.448
2wxvWXVCyclin-dependent kinase 22.7.11.220.448
3a7jADPSerine/threonine-protein kinase 242.7.11.10.448
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3t3r9PLCytochrome P450 2A61.14.130.448
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.448
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.448
4o2bLOCTubulin beta-2B chain/0.448
4wecNADShort chain dehydrogenase/0.448
1diuBDMDihydrofolate reductase1.5.1.30.447
1py5PY1TGF-beta receptor type-12.7.11.300.447
1s19MC9Vitamin D3 receptor/0.447
1txiTX5Vitamin D3 receptor/0.447
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.447
2he5NDPAldo-keto reductase family 1 member C211.1.10.447
2tpsTPSThiamine-phosphate synthase/0.447
2v58LZJBiotin carboxylase6.3.4.140.447
2wotZZGTGF-beta receptor type-12.7.11.300.447
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.447
3gwfNAPCyclohexanone monooxygenase/0.447
3ibqATPPyridoxal kinase/0.447
4jicFMNGTN Reductase/0.447
5e92ANPTGF-beta receptor type-22.7.11.300.447
1dirNADDihydropteridine reductase1.5.1.340.446
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.446
1u9iATPCircadian clock protein kinase KaiC2.7.11.10.446
2avvMK1Gag-Pol polyprotein3.4.23.160.446
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
2ociTYCValacyclovir hydrolase3.10.446
2zjmF1MBeta-secretase 13.4.23.460.446
3a783EVVitamin D3 receptor/0.446
3eej53RUncharacterized protein/0.446
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.446
3r9uFADThioredoxin reductase/0.446
4g2fC07Ephrin type-A receptor 32.7.10.10.446
4hgs15GCasein kinase I isoform gamma-32.7.11.10.446
4mwhATPCasein kinase II subunit alpha2.7.11.10.446
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.446
1b2lNDCAlcohol dehydrogenase1.1.1.10.445
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1likADNAdenosine kinase2.7.1.200.445
1omoNADAlanine dehydrogenase/0.445
1yrcCAMCamphor 5-monooxygenase1.14.15.10.445
2dq7STUTyrosine-protein kinase Fyn2.7.10.20.445
2dr3ADPUPF0273 protein PH0284/0.445
2e9uA25Serine/threonine-protein kinase Chk12.7.11.10.445
2izrBRKCasein kinase I isoform gamma-32.7.11.10.445
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.445
2p5uNADUDP-glucose 4-epimerase/0.445
2q9fC3SCholesterol 24-hydroxylase/0.445
2rqfJH3Hemolymph juvenile hormone binding protein/0.445
3gueUPGUTP-glucose-1-phosphate uridylyltransferase 2, putative/0.445
3nl6TPSUncharacterized protein/0.445
3pd3A3TThreonine--tRNA ligase6.1.1.30.445
3qt62P0Mevalonate diphosphate decarboxylase/0.445
3r324CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.445
3slkNDPPolyketide synthase extender module 2/0.445
3w0gW07Vitamin D3 receptor/0.445
4fuyEK2Mitogen-activated protein kinase 12.7.11.240.445
4gk2L66Ephrin type-A receptor 32.7.10.10.445
4ienCOAPutative acyl-CoA hydrolase/0.445
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.445
4n57ADPAPH(2'')-Id/0.445
4qmySTUSerine/threonine-protein kinase 242.7.11.10.445
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1jm6ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.444
1n3rGTPGTP cyclohydrolase 13.5.4.160.444
2bunFADAppA protein/0.444
2pziAXXSerine/threonine-protein kinase PknG2.7.11.10.444
2x7hPFNProstaglandin reductase 310.444
3ac3KSHTyrosine-protein kinase Lck2.7.10.20.444
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.444
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.444
3ns2PYVAbscisic acid receptor PYL2/0.444
4lb2DM5Serum albumin/0.444
4tmcFMNOld yellow enzyme/0.444
5a3bAPRSIR2 family protein/0.444
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
2d8aNADL-threonine 3-dehydrogenase/0.443
2xyuQ9GEphrin type-A receptor 42.7.10.10.443
2z3uCRRCytochrome P450/0.443
3drcMTXDihydrofolate reductase1.5.1.30.443
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3l8p0CEAngiopoietin-1 receptor2.7.10.10.443
4dpuAGSMevalonate diphosphate decarboxylase/0.443
4mgiCMPRap guanine nucleotide exchange factor 4/0.443
4prvADPDNA gyrase subunit B/0.443
4u7wNDPMxaA/0.443
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.442
1fxsNAPGDP-L-fucose synthase/0.442
1g6cIFPThiamine-phosphate synthase/0.442
1lnyIMOAdenylosuccinate synthetase isozyme 1/0.442
1nhhANPDNA mismatch repair protein MutL/0.442
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1um0FMNChorismate synthase/0.442
2itxANPEpidermal growth factor receptor2.7.10.10.442
2py3ACPFibroblast growth factor receptor 2/0.442
2z0x5CAUncharacterized protein/0.442
3hk1B64Fatty acid-binding protein, adipocyte/0.442
3p8iFMNPentaerythritol tetranitrate reductase/0.442
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4fizCUE17beta-hydroxysteroid dehydrogenase/0.442
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.442
5fwnNAPPutative dehydrogenase/0.442
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1dz6CAMCamphor 5-monooxygenase1.14.15.10.441
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.441
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.441
1llwFMNFerredoxin-dependent glutamate synthase 21.4.7.10.441
1me8RVPInosine-5'-monophosphate dehydrogenase/0.441
1qpdSTUTyrosine-protein kinase Lck2.7.10.20.441
1r2jFADFkbI/0.441
1uyuCAMCamphor 5-monooxygenase1.14.15.10.441
1yw2PGJMitogen-activated protein kinase 14/0.441
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.441
2oapANPType II secretion system protein (GspE-2)/0.441
2qboCAMCamphor 5-monooxygenase1.14.15.10.441
2v59LZKBiotin carboxylase6.3.4.140.441
2zdt46CMitogen-activated protein kinase 102.7.11.240.441
3iphG11Mitogen-activated protein kinase 14/0.441
3kruFMNNADH:flavin oxidoreductase/NADH oxidase/0.441
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.441
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
4hyu1BKMitogen-activated protein kinase 82.7.11.240.441
4kxn6K62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.441
1e3eNAIAlcohol dehydrogenase 41.1.1.10.440
1phhFADp-hydroxybenzoate hydroxylase/0.440
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.440
2gjnFMNNitronate monooxygenase1.13.12.160.440
2hy81STSerine/threonine-protein kinase PAK 12.7.11.10.440
2j9gANPBiotin carboxylase6.3.4.140.440
2qblCAMCamphor 5-monooxygenase1.14.15.10.440
2qbmCAMCamphor 5-monooxygenase1.14.15.10.440
2wouZZFTGF-beta receptor type-12.7.11.300.440
3cd57HI3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.440
3cluFADElectron transfer flavoprotein subunit alpha/0.440
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3orfNADDihydropteridine reductase1.5.1.340.440
3to3ATPPetrobactin biosynthesis protein AsbB/0.440
3vthAPCCarbamoyltransferase/0.440
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.440
4i231C9Epidermal growth factor receptor2.7.10.10.440
4j97ACPFibroblast growth factor receptor 2/0.440
4kxl6C62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.440
4riyADPEpidermal growth factor receptor2.7.10.10.440
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.440
4y9qC2EUncharacterized protein/0.440