Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
1av5AP2Histidine triad nucleotide-binding protein 13

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1av5AP2Histidine triad nucleotide-binding protein 131.000
1rzy5ASHistidine triad nucleotide-binding protein 130.614
4eqgA5AHistidine triad nucleotide-binding protein 130.569
5i2fBS5Histidine triad nucleotide-binding protein 130.567
3oxk5GPHistidine triad nucleotide-binding protein30.557
3qgzADNHistidine triad nucleotide-binding protein 130.552
4eqeKAAHistidine triad nucleotide-binding protein 130.538
5fitAP2Bis(5'-adenosyl)-triphosphatase3.6.1.290.514
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.498
5c8d5ADProbable transcriptional regulator/0.496
3juoAJDPhenazine biosynthesis protein A/B/0.495
3l0lHC3Nuclear receptor ROR-gamma/0.492
2z3uCRRCytochrome P450/0.486
3gkjHC3Niemann-Pick C1 protein/0.486
3n1t5GPPurine nucleoside phosphoramidase/0.484
1o6rR19Squalene--hopene cyclase4.2.1.1290.483
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.483
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.483
1xduSFGAclacinomycin 10-hydroxylase RdmB4.1.10.482
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.481
1nhkCMPNucleoside diphosphate kinase2.7.4.60.480
1fwkADPHomoserine kinase2.7.1.390.479
3cid318Beta-secretase 13.4.23.460.479
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.479
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.477
3cic316Beta-secretase 13.4.23.460.476
4az0S61Lysosomal protective protein3.4.16.50.476
2iqgF2IBeta-secretase 13.4.23.460.475
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.474
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.473
3cib314Beta-secretase 13.4.23.460.473
1uydPU8Heat shock protein HSP 90-alpha/0.472
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.472
4egu5GPPutative histidine triad (HIT) protein/0.472
2vbpVB1Isopenicillin N synthase1.21.3.10.471
3gwfNAPCyclohexanone monooxygenase/0.471
4gkvNADAlcohol dehydrogenase, propanol-preferring1.1.1.10.471
3acy702Dehydrosqualene synthase/0.470
3hf6LX0Tryptophan 5-hydroxylase 11.14.16.40.470
3lpkZ76Beta-secretase 13.4.23.460.470
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
4h5cYS4Farnesyl pyrophosphate synthase2.5.1.100.468
4iaq2GM5-hydroxytryptamine receptor 1B/0.468
2gd0MRSProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.467
3n1s5GPPurine nucleoside phosphoramidase/0.467
3uwlFOZThymidylate synthase/0.467
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.466
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.466
3ixj586Beta-secretase 13.4.23.460.466
3lpiZ74Beta-secretase 13.4.23.460.466
3nmhPYVAbscisic acid receptor PYL2/0.466
3kytHC2Nuclear receptor ROR-gamma/0.465
1h36R88Squalene--hopene cyclase4.2.1.1290.464
1rf7DHFDihydrofolate reductase1.5.1.30.463
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.463
2p83MR0Beta-secretase 13.4.23.460.463
3c3dFO12-phospho-L-lactate transferase/0.463
3ou7SAMSAM-dependent methyltransferase/0.463
2idkC2FGlycine N-methyltransferase2.1.1.200.462
3a1l2CCCytochrome P450/0.462
3w8wFADPutative FAD-dependent oxygenase EncM/0.462
4c49HCYCorticosteroid-binding globulin/0.462
1it7GUNtRNA-guanine(15) transglycosylase2.4.2.480.461
2i4tUA2Purine nucleoside phosphorylase, putative/0.461
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.461
4h5eYS4Farnesyl pyrophosphate synthase2.5.1.100.461
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
3hf8ML0Tryptophan 5-hydroxylase 11.14.16.40.460
3zeiAWHO-acetylserine sulfhydrylase/0.460
1t7o152Carnitine O-acetyltransferase2.3.1.70.459
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.459
1jomFFODihydrofolate reductase1.5.1.30.458
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.458
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
3ohh3HHBeta-secretase 13.4.23.460.458
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.458
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.457
4pnmNU1Tankyrase-22.4.2.300.457
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.457
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.456
2fk8SAMHydroxymycolate synthase MmaA42.1.10.456
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.456
2o7pNAPRiboflavin biosynthesis protein RibD/0.456
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.456
3dm6757Beta-secretase 13.4.23.460.456
4ap0ADPKinesin-like protein KIF11/0.456
1t0iFMNNAD(P)H-dependent FMN reductase LOT6/0.455
2bp1NDPAflatoxin B1 aldehyde reductase member 2/0.455
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
3e2sFADBifunctional protein PutA1.5.5.20.455
3zecANPAdenosine monophosphate-protein transferase SoFic2.7.7.n10.455
5bp9SAHPutative methyltransferase protein/0.455
5k2cZMAAdenosine receptor A2a/0.455
1disBDMDihydrofolate reductase1.5.1.30.454
1diuBDMDihydrofolate reductase1.5.1.30.454
1v2hGUNPurine nucleoside phosphorylase2.4.2.10.454
3c35KAIGlutamate receptor ionotropic, kainate 1/0.454
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
3zkuHCVIsopenicillin N synthase1.21.3.10.454
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.454
4phlPILPhosphodiesterase/0.454
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
1ygkRRCPyridoxal kinase2.7.1.350.453
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
3gkiCLRNiemann-Pick C1 protein/0.453
3q9bB3NAcetylpolyamine amidohydrolase/0.453
3ujlA8SAbscisic acid receptor PYL2/0.453
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.453
4qi9MTXDihydrofolate reductase/0.453
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.453
4yklGMPAprataxin-like protein30.453
1lf3EH5Plasmepsin-23.4.23.390.452
1m9nAMZBifunctional purine biosynthesis protein PURH2.1.2.30.452
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
3f3y4OABile salt sulfotransferase2.8.2.140.452
3u8dU8DPhospholipase A2, membrane associated/0.452
3w0uHPWLactoylglutathione lyase4.4.1.50.452
4a9mP9MBromodomain-containing protein 2/0.452
4bj9UHBTankyrase-22.4.2.300.452
2y6fM9FIsopenicillin N synthase1.21.3.10.451
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.451
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.451
3k5gBJCBeta-secretase 13.4.23.460.451
3nj0PYVAbscisic acid receptor PYL2/0.451
3pg3DG7Mitogen-activated protein kinase 14/0.451
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.451
4ea2RWZDehydrosqualene synthase/0.451
4muw2F4cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4qzuRTLRetinol-binding protein 2/0.451
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.451
1ek2CDUBifunctional epoxide hydrolase 2/0.450
1icqOPD12-oxophytodienoate reductase 11.3.1.420.450
1nbiSAMGlycine N-methyltransferase2.1.1.200.450
1s0xC3SNuclear receptor ROR-alpha/0.450
1zw9H64ATP-dependent molecular chaperone HSP82/0.450
2fzhDH1Dihydrofolate reductase1.5.1.30.450
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.450
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.450
2vbdV10Isopenicillin N synthase1.21.3.10.450
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.450
3qls55VDihydrofolate reductase1.5.1.30.450
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.450
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.450
4i5vB4PDiadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2/0.450
4k88HFGBifunctional glutamate/proline--tRNA ligase6.1.1.150.450
4v2gCTCTetracycline repressor protein class D/0.450
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.450
1ygjRMCPyridoxal kinase2.7.1.350.449
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.449
2ohhFMNType A flavoprotein FprA10.449
2tctCTCTetracycline repressor protein class D/0.449
2ydoADNAdenosine receptor A2a/0.449
4dh60KNBeta-secretase 13.4.23.460.449
4ez8DHFThymidylate synthase2.1.1.450.449
4if5ACOAlpha-tubulin N-acetyltransferase 1/0.449
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.449
5ab7MLCNonspecific lipid-transfer protein, putative/0.449
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.448
1rc4DDFDihydrofolate reductase1.5.1.30.448
1suiFRECaffeoyl-CoA O-methyltransferase2.1.1.1040.448
2a4xBLMMitomycin-binding protein/0.448
3hxeBD8Geranylgeranyl transferase type-2 subunit beta2.5.1.600.448
3w0c6DSVitamin D3 receptor/0.448
4az3S35Lysosomal protective protein3.4.16.50.448
4deg0JJHepatocyte growth factor receptor2.7.10.10.448
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.448
4lrrCF9Thymidylate synthase/0.448
4ydqHFGProline--tRNA ligase6.1.1.150.448
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.448
1z7yAA5Cysteine synthase 12.5.1.470.447
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.447
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.447
3hziATPSerine/threonine-protein kinase toxin HipA/0.447
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.447
4at0FADPossible succinate dehydrogenase/0.447
4lc71WPBeta-secretase 13.4.23.460.447
4xe606UDihydrofolate reductase1.5.1.30.447
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.446
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2g94ZPQBeta-secretase 13.4.23.460.446
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.446
2qd5CHDFerrochelatase, mitochondrial4.99.1.10.446
3c3eGDP2-phospho-L-lactate transferase/0.446
3exo5MSBeta-secretase 13.4.23.460.446
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4ifvT27Gag-Pol polyprotein2.7.7.490.446
4ivrN50Thymidine kinase/0.446
4o8aFADBifunctional protein PutA1.2.1.880.446
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.446
1khrCOAStreptogramin A acetyltransferase2.3.10.445
2rhrEMOPutative ketoacyl reductase1.3.10.445
2wn6NDPADP-ribosyltransferase enzymatic component/0.445
3bsyACOUDP-N-acetylbacillosamine N-acetyltransferase2.3.1.2030.445
3c36KAIGlutamate receptor ionotropic, kainate 1/0.445
3o9lLPNRenin3.4.23.150.445
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.445
3up0D7SaceDAF-12/0.445
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.445
4dpi0N1Beta-secretase 13.4.23.460.445
4kfj1R0Dihydrofolate reductase1.5.1.30.445
4qmpDKISerine/threonine-protein kinase 242.7.11.10.445
5kf9ACOPredicted acetyltransferase/0.445
5k2aZMAAdenosine receptor A2a/0.445
1eqbFFOSerine hydroxymethyltransferase2.1.2.10.444
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.444
1rgsCMPcAMP-dependent protein kinase type I-alpha regulatory subunit/0.444
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.444
1ychFMNNitric oxide reductase10.444
2bktRPFRenin3.4.23.150.444
2e9dB76Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
2isc223Purine nucleoside phosphorylase, putative/0.444
2y1w849Histone-arginine methyltransferase CARM1/0.444
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
3up3XCAaceDAF-12/0.444
3vtbTKAVitamin D3 receptor/0.444
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
3zsh469Mitogen-activated protein kinase 14/0.444
4a87NARMajor pollen allergen Bet v 1-A/0.444
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
5k2bZMAAdenosine receptor A2a/0.444
1fcy564Retinoic acid receptor gamma/0.443
1kyzFERCaffeic acid 3-O-methyltransferase2.1.1.680.443
1mgoNADAlcohol dehydrogenase E chain1.1.1.10.443
2ay84TBAromatic-amino-acid aminotransferase2.6.1.570.443
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3fhxPXLPyridoxal kinase2.7.1.350.443
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.443
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.443
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.443
3my5RFZCyclin-dependent kinase 22.7.11.220.443
3qj5022Alcohol dehydrogenase class-31.1.1.10.443
3u3o3QVSulfotransferase 1A12.8.2.10.443
4f6xZYLDehydrosqualene synthase/0.443
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4hr2ADPNucleoside diphosphate kinase/0.443
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
4onqSFGDNA methyltransferase/0.443
4rv9SAHD-mycarose 3-C-methyltransferase/0.443
5ab6CAANonspecific lipid-transfer protein, putative/0.443
5k2dZMAAdenosine receptor A2a/0.443
1e2jTHMThymidine kinase/0.442
1exa394Retinoic acid receptor gamma/0.442
1fcx184Retinoic acid receptor gamma/0.442
1nvtNAPShikimate dehydrogenase (NADP(+))/0.442
1uyePU9Heat shock protein HSP 90-alpha/0.442
2dxdANPNucleoside diphosphate kinase2.7.4.60.442
2g0bNLTLong-chain N-acyl amino acid synthase/0.442
3deiRXBCaspase-33.4.22.560.442
3dejRXCCaspase-33.4.22.560.442
3ei8PL5LL-diaminopimelate aminotransferase, chloroplastic/0.442
3r5yF42Uncharacterized protein/0.442
3upyFOMOxidoreductase, putative/0.442
3v0o4GWHisto-blood group ABO system transferase/0.442
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.442
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
4ckcSAHmRNA-capping enzyme catalytic subunit2.1.1.560.442
4d2dALA_ALA_ALADi-or tripeptide:H+ symporter/0.442
4pkhADPActin, alpha skeletal muscle/0.442
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.442
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
1iyzNDPProbable quinone oxidoreductase/0.441
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.441
1kgjFL8Transthyretin/0.441
1oc1ASVIsopenicillin N synthase1.21.3.10.441
1pz1NAPGeneral stress protein 69/0.441
1tj2FADBifunctional protein PutA1.5.5.20.441
1u1d181Uridine phosphorylase2.4.2.30.441
2aclL05Oxysterols receptor LXR-alpha/0.441
2bgjFADNADPH:ferredoxin reductase/0.441
2fmn4HF5,10-methylenetetrahydrofolate reductase1.5.1.200.441
2uw0GVKcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2vkmBSDBeta-secretase 13.4.23.460.441
3skgPB8Beta-secretase 13.4.23.460.441
3vaqADNPutative adenosine kinase/0.441
3vg9ZMAAdenosine receptor A2a/0.441
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.441
4fizCUE17beta-hydroxysteroid dehydrogenase/0.441
4h9506UDihydrofolate reductase1.5.1.30.441
4l17DNQGlutamate receptor 2/0.441
4lb2DM5Serum albumin/0.441
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
5iu86DZAdenosine receptor A2a/0.441
1b87ACOAac(6')-Ii protein/0.440
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
1pydTDPPyruvate decarboxylase isozyme 1/0.440
2clfF6FTryptophan synthase alpha chain/0.440
2d0kFOLDihydrofolate reductase1.5.1.30.440
2dw4FADLysine-specific histone demethylase 1A10.440
2ejzSAHDiphthine synthase/0.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.440
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4a83DXCMajor pollen allergen Bet v 1-A/0.440
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4elb34RDihydrofolate reductase/0.440
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4h3g10QBeta-secretase 13.4.23.460.440
4jvj1MVFarnesyl pyrophosphate synthase2.5.1.100.440
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
5f2kSAHUncharacterized protein/0.440
5jtbZMAAdenosine receptor A2a/0.440