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
2v1aFMNNPH1-1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2v1aFMNNPH1-1/1.000
2v0uFMNNPH1-1/0.688
5efwFMNNPH1-1/0.568
5djtFMNNPH1-2/0.554
4eepFMNPhototropin-22.7.11.10.543
1g28FMNPHY3/0.542
4eerFMNPhototropin-22.7.11.10.527
4eesFMNPhototropin-22.7.11.10.523
4hj6FMNLOV protein/0.516
4eetFMNPhototropin-22.7.11.10.507
2pd8FADVivid PAS protein VVD/0.499
2pd7FADVivid PAS protein VVD/0.489
3lqfNADGalactitol dehydrogenase/0.487
1n9lFMNPutative blue light receptor/0.484
2gjnFMNNitronate monooxygenase1.13.12.160.484
5dp2NAPCurF/0.484
4echFADPolyamine oxidase FMS1/0.483
4hiaFMNLOV protein/0.482
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.481
2z6cFMNPhototropin-12.7.11.10.481
4kuoRBFPutative blue-light photoreceptor/0.481
2hckQUETyrosine-protein kinase HCK2.7.10.20.480
4gt8ADPSensor protein VraS2.7.13.30.480
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.477
2e16SAHDiphthine synthase/0.475
4hj4FMNLOV protein/0.475
4kukRBFPutative blue-light photoreceptor/0.474
1dr3TAPDihydrofolate reductase1.5.1.30.473
2ejzSAHDiphthine synthase/0.473
3ske054Genome polyprotein2.7.7.480.472
2xlrFADPutative flavin-containing monooxygenase/0.470
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.469
1thnADPAnti-sigma F factor/0.468
3slkNDPPolyketide synthase extender module 2/0.468
4r3aRBFBlue-light-activated histidine kinase 22.7.13.30.468
3gfbNADL-threonine 3-dehydrogenase/0.467
4eeuFMNPhototropin-22.7.11.10.467
4f650S9Fibroblast growth factor receptor 1/0.467
1dr3HBIDihydrofolate reductase1.5.1.30.466
2briANPUridylate kinase2.7.4.220.466
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.466
4hhdFMNPhototropin-12.7.11.10.466
3evbSAHGenome polyprotein2.1.1.560.465
1i59ANPChemotaxis protein CheA2.7.13.30.464
1i59ADPChemotaxis protein CheA2.7.13.30.464
3clsFADElectron transfer flavoprotein subunit alpha/0.464
2emuSAHDiphthine synthase/0.463
2pdtFADVivid PAS protein VVD/0.463
3h3r14HCollagen type IV alpha-3-binding protein/0.463
3h3sH15Collagen type IV alpha-3-binding protein/0.463
1tilATPAnti-sigma F factor/0.462
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.462
3s55NADPutative short-chain dehydrogenase/reductase/0.462
2rcyNAPPyrroline-5-carboxylate reductase/0.461
3h3t16HCollagen type IV alpha-3-binding protein/0.461
3is2FADVivid PAS protein VVD/0.461
4r1lADPPhenylacetate-coenzyme A ligase/0.461
4r38RBFBlue-light-activated histidine kinase 22.7.13.30.461
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.461
1p0pBCHCholinesterase3.1.1.80.460
2ejvNADL-threonine 3-dehydrogenase/0.460
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.460
3nl6TPSUncharacterized protein/0.460
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.460
4z24FADPutative GMC-type oxidoreductase R13510.460
1hb1OCVIsopenicillin N synthase1.21.3.10.459
3hjkFADVivid PAS protein VVD/0.459
4k28NADShikimate dehydrogenase family protein/0.459
4prxADPDNA gyrase subunit B/0.459
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
2ou2ACOHistone acetyltransferase KAT5/0.458
4b7754MBeta-secretase 13.4.23.460.458
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.457
2z6dFMNPhototropin-22.7.11.10.457
3wv9FEGHmd co-occurring protein HcgE/0.457
3zoiM2WIsopenicillin N synthase1.21.3.10.457
3zv64HBCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.457
4acuQN7Beta-secretase 13.4.23.460.457
3l5dBDVBeta-secretase 13.4.23.460.456
4dpy2P0Mevalonate diphosphate decarboxylase/0.456
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.456
1gqtACPRibokinase/0.455
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.455
2ek2SAHDiphthine synthase/0.455
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.455
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.455
1g1aNADdTDP-glucose 4,6-dehydratase/0.454
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.454
2eh4SAHDiphthine synthase/0.454
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.454
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
4friDWABeta-secretase 13.4.23.460.454
4l17DNQGlutamate receptor 2/0.454
4l4fCAMCamphor 5-monooxygenase1.14.15.10.454
4wucANPDNA gyrase subunit B/0.454
4wudANPDNA gyrase subunit B/0.454
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1sbrVIBPutative HMP/thiamine-binding protein YkoF/0.453
2en5SAHDiphthine synthase/0.453
2g8yNADHydroxycarboxylate dehydrogenase B/0.453
2iviACWIsopenicillin N synthase1.21.3.10.453
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.453
2y60M8FIsopenicillin N synthase1.21.3.10.453
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.453
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.453
1pqc444Oxysterols receptor LXR-beta/0.452
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.452
1wngSAHDiphthine synthase/0.452
2rgoFADAlpha-Glycerophosphate Oxidase/0.452
3k8q22APurine nucleoside phosphorylase2.4.2.10.452
3zkyWT4Isopenicillin N synthase1.21.3.10.452
4b1rITCTetracycline repressor protein class D/0.452
4pleCPSNuclear receptor subfamily 5 group A member 2/0.452
1bk0ACVIsopenicillin N synthase1.21.3.10.451
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.451
1ot7CHCBile acid receptor/0.451
1udaUFGUDP-glucose 4-epimerase5.1.3.20.451
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.451
2owgSAHDiphthine synthase/0.451
2pb4SAHDiphthine synthase/0.451
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.451
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.451
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.451
3h06VBPGlutamate receptor 2/0.451
3qwbNDPProbable quinone oxidoreductase1.6.5.50.451
4bfxZVXPantothenate kinase2.7.1.330.451
4du82P0Mevalonate diphosphate decarboxylase/0.451
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
4hnbFMNLOV protein/0.451
1ay0TPPTransketolase 12.2.1.10.450
1drhNAPDihydrofolate reductase1.5.1.30.450
1i5bANPChemotaxis protein CheA2.7.13.30.450
1jpaANPEphrin type-B receptor 22.7.10.10.450
1uzwCDHIsopenicillin N synthase1.21.3.10.450
2gjlFMNNitronate monooxygenase1.13.12.160.450
2xhrC0PHeat shock protein HSP 90-alpha/0.450
3d4pNADL-lactate dehydrogenase 11.1.1.270.450
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.450
4ih71ERGenome polyprotein2.7.7.480.450
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.449
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.449
2oc4IMHPurine nucleoside phosphorylase2.4.2.10.449
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
3qlsNDPDihydrofolate reductase1.5.1.30.449
3w5rLOAVitamin D3 receptor/0.449
4l4xNDPAmphI/0.449
5a3bAPRSIR2 family protein/0.449
6coxS58Prostaglandin G/H synthase 21.14.99.10.449
1osvCHCBile acid receptor/0.448
1s3uTQDDihydrofolate reductase1.5.1.30.448
2ed5SAHDiphthine synthase/0.448
2ek7SAHDiphthine synthase/0.448
2z4sADPChromosomal replication initiator protein DnaA/0.448
3hl0NADMaleylacetate reductase/0.448
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.448
3w32W32Epidermal growth factor receptor2.7.10.10.448
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.448
4fvqATPTyrosine-protein kinase JAK2/0.448
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
5i4nATPTyrosine-protein kinase JAK2/0.448
1nzfUPGDNA beta-glucosyltransferase/0.447
1zq5E04Aldo-keto reductase family 1 member C3/0.447
2dv4SAHDiphthine synthase/0.447
2dv7SAHDiphthine synthase/0.447
2npaMMBPeroxisome proliferator-activated receptor alpha/0.447
2owfSAHDiphthine synthase/0.447
3b6zCO7Enoyl reductase LovC10.447
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3nbvANPKetohexokinase/0.447
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.447
4a862ANMajor pollen allergen Bet v 1-A/0.447
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.447
4lb2DM5Serum albumin/0.447
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.447
1blzACVIsopenicillin N synthase1.21.3.10.446
1go2FADFerredoxin--NADP reductase1.18.1.20.446
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1x8lOXRRetinol dehydratase/0.446
1xkkFMMEpidermal growth factor receptor2.7.10.10.446
2b7aIZATyrosine-protein kinase JAK2/0.446
2bxmIMNSerum albumin/0.446
3a0tADPSensor histidine kinase/0.446
3w4yFADMitochondrial FAD-linked sulfhydryl oxidase ERV11.8.3.20.446
4b5pACOAlpha-tubulin N-acetyltransferase 1/0.446
4ha6PXMPyridoxine 4-oxidase/0.446
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.446
1meiXMPInosine-5'-monophosphate dehydrogenase/0.445
1nzdUPGDNA beta-glucosyltransferase/0.445
1pzfA3DLactate dehydrogenase/0.445
1rfuADPPyridoxal kinase2.7.1.350.445
1t88CAMCamphor 5-monooxygenase1.14.15.10.445
1w06W05Isopenicillin N synthase1.21.3.10.445
2a1mCAMCamphor 5-monooxygenase1.14.15.10.445
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.445
2vw5BC6ATP-dependent molecular chaperone HSP82/0.445
2yy8SAMtRNA (cytidine(56)-2'-O)-methyltransferase/0.445
3gtsD3MDdmC/0.445
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.445
4q71FADBifunctional protein PutA/0.445
5j4eFMNSensory box protein/0.445
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
1qiqACCIsopenicillin N synthase1.21.3.10.444
1vzdCB3Thymidylate synthase/0.444
1xkdNAPIsocitrate dehydrogenase [NADP]/0.444
2ejkSAHDiphthine synthase/0.444
2vd0D27Hematopoietic prostaglandin D synthase/0.444
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.444
3phiNDPShikimate dehydrogenase (NADP(+))/0.444
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.444
4ji91M3Tyrosine-protein kinase JAK2/0.444
4m9aFDAAcyl-CoA dehydrogenase/0.444
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.444
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.444
1dg8NDPDihydrofolate reductase1.5.1.30.443
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.443
1qorNDPQuinone oxidoreductase 1/0.443
1s7gNADNAD-dependent protein deacylase 2/0.443
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.443
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
2dvlFADAcyl-CoA dehydrogenase/0.443
2egsSAHDiphthine synthase/0.443
2pchSAHDiphthine synthase/0.443
2qboCAMCamphor 5-monooxygenase1.14.15.10.443
2rhrEMOPutative ketoacyl reductase1.3.10.443
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
2y05NAPProstaglandin reductase 1/0.443
3cgcCOACoenzyme A disulfide reductase/0.443
3cgdCOACoenzyme A disulfide reductase/0.443
3p0fBAUUridine phosphorylase 22.4.2.30.443
4a8v2ANMajor pollen allergen Bet v 1-J/0.443
4l7vSAHProtein-L-isoaspartate O-methyltransferase/0.443
4u8iFDAUDP-galactopyranose mutase/0.443
5a3cNADSIR2 family protein/0.443
1f28UMPThymidylate synthase2.1.1.450.442
2ahrNAPPyrroline-5-carboxylate reductase/0.442
2dxvSAHDiphthine synthase/0.442
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.442
2pciSAHDiphthine synthase/0.442
2q5oPPYIndole-3-pyruvate decarboxylase4.1.1.740.442
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
2zgzGNPPlasmid segregation protein ParM/0.442
3cukFADD-amino-acid oxidase1.4.3.30.442
3dolGWIPol protein/0.442
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.442
4jqlVJ6Heat shock protein HSP 90-alpha/0.442
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.442
4relKMPGlycosyltransferase/0.442
4uyf73BBromodomain-containing protein 2/0.442
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.441
1jolFFODihydrofolate reductase1.5.1.30.441
1o76CAMCamphor 5-monooxygenase1.14.15.10.441
1qgyFADFerredoxin--NADP reductase1.18.1.20.441
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.441
2a1oCAMCamphor 5-monooxygenase1.14.15.10.441
2e0nSAHPrecorrin-2 C20-methyltransferase/0.441
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2mwgFMNBlue-light photoreceptor/0.441
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.441
3cntFADPolyamine oxidase FMS1/0.441
3d84NDPDihydrofolate reductase1.5.1.30.441
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.441
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.441
4a5lFADThioredoxin reductase/0.441
4dc1NDPPutative ketoacyl reductase1.3.10.441
4fryNADPutative signal-transduction protein with CBS domains/0.441
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.440
1me6IVSPlasmepsin-23.4.23.390.440
1pzgA3DLactate dehydrogenase/0.440
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.440
2dv3SAHDiphthine synthase/0.440
2el0SAHDiphthine synthase/0.440
3vrwYS5Vitamin D3 receptor/0.440
4a802ANMajor pollen allergen Bet v 1-A/0.440
4njoNADD-3-phosphoglycerate dehydrogenase, putative/0.440
4y0kNAPAntE/0.440