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
4at2ASDPossible succinate dehydrogenase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4at2ASDPossible succinate dehydrogenase/1.000
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.510
1qxlFR8Adenosine deaminase3.5.4.40.498
2fpcSCGStrictosidine synthase4.3.3.20.494
1txiTX5Vitamin D3 receptor/0.487
3w0c6DSVitamin D3 receptor/0.487
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.485
1fmjRTLRetinol dehydratase/0.484
2vuw5IDSerine/threonine-protein kinase haspin2.7.11.10.481
3kpzZNEVitamin D3 receptor/0.481
1ie9VDXVitamin D3 receptor/0.480
2zbaZBATrichothecene 3-O-acetyltransferase/0.480
4bcoT6QCyclin-dependent kinase 22.7.11.220.480
4mmf29QNa(+):neurotransmitter symporter (Snf family)/0.480
2x1nX1NCyclin-dependent kinase 22.7.11.220.479
2i40BLZCyclin-dependent kinase 22.7.11.220.477
4bcpT3CCyclin-dependent kinase 22.7.11.220.476
2uzbC75Cyclin-dependent kinase 22.7.11.220.475
1klkPMDDihydrofolate reductase1.5.1.30.474
3u9n09HSerine/threonine-protein kinase Chk12.7.11.10.474
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.474
2y7jB49Phosphorylase b kinase gamma catalytic chain, liver/testis isoform2.7.11.190.473
3iw4LW4Protein kinase C alpha type2.7.11.130.472
4nc3ERM5-hydroxytryptamine receptor 2B/0.471
3nj0PYVAbscisic acid receptor PYL2/0.470
3ns2PYVAbscisic acid receptor PYL2/0.470
1ie8KH1Vitamin D3 receptor/0.469
1ndzFR5Adenosine deaminase3.5.4.40.468
4eilUMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.468
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.467
2hc4VDXVitamin D3 receptor A/0.466
4bcqTJFCyclin-dependent kinase 22.7.11.220.466
4klaCHDFerrochelatase, mitochondrial4.99.1.10.465
1vj3TABDihydrofolate reductase1.5.1.30.464
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
2z7gEH9Adenosine deaminase3.5.4.40.464
4gg70J8Hepatocyte growth factor receptor2.7.10.10.464
4iyg1HUStrictosidine synthase4.3.3.20.464
5jadFB2Platelet-activating factor acetylhydrolase3.1.1.470.464
3vt5YI2Vitamin D3 receptor/0.463
2hamC33Vitamin D3 receptor/0.462
3c3dFO12-phospho-L-lactate transferase/0.462
4n702HXSerine/threonine-protein kinase pim-12.7.11.10.462
1aq1STUCyclin-dependent kinase 22.7.11.220.461
1j3iWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
2blaCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
1e9hINRCyclin-dependent kinase 22.7.11.220.460
3b5iSAHIndole-3-acetate O-methyltransferase 1/0.460
3njoPYVAbscisic acid receptor PYR1/0.460
4oacADPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.460
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.460
5eccNAPDehydrofolate reductase type I/0.460
2b00GCHPhospholipase A2, major isoenzyme3.1.1.40.459
4xe606UDihydrofolate reductase1.5.1.30.459
1v7aFRCAdenosine deaminase3.5.4.40.458
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.458
2hb7O1CVitamin D3 receptor/0.458
2o65MYFSerine/threonine-protein kinase pim-12.7.11.10.458
2vagV25Dual specificity protein kinase CLK12.7.12.10.458
4bchT7ZCyclin-dependent kinase 92.7.11.220.458
4c02TAKActivin receptor type-12.7.11.300.458
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
4h9506UDihydrofolate reductase1.5.1.30.458
1h1pCMGCyclin-dependent kinase 22.7.11.220.457
3cseN22Uncharacterized protein/0.457
3nizADPCdc2-like CDK2/CDC28 like protein kinase/0.457
3qly55VUncharacterized protein/0.457
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
2vrbNAPTriphenylmethane reductase/0.456
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
3qn1A8SAbscisic acid receptor PYR1/0.456
4ds8A8SAbscisic acid receptor PYL3/0.456
4jqeANPCasein kinase II subunit alpha2.7.11.10.456
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.455
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.455
2v58LZJBiotin carboxylase6.3.4.140.455
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.455
4iteTEYVitamin D3 receptor/0.455
1s0zEB1Vitamin D3 receptor/0.454
1tvrTB9Gag-Pol polyprotein2.7.7.490.454
2ociTYCValacyclovir hydrolase3.10.454
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
3vtdTKDVitamin D3 receptor/0.454
4aojV4ZHigh affinity nerve growth factor receptor2.7.10.10.454
4fhh0U3Vitamin D3 receptor A/0.454
4g1z0VPVitamin D3 receptor A/0.454
1m78CLZDihydrofolate reductase1.5.1.30.453
2giuFBREstrogen receptor beta/0.453
2oaxSNLMineralocorticoid receptor/0.453
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.453
2wihP48Cyclin-dependent kinase 22.7.11.220.453
3v1s0LHStrictosidine synthase4.3.3.20.453
4g1y0VOVitamin D3 receptor A/0.453
1dajMOTDihydrofolate reductase1.5.1.30.452
1nhz486Glucocorticoid receptor/0.452
2btsU32Cyclin-dependent kinase 22.7.11.220.452
2c5nCK8Cyclin-dependent kinase 22.7.11.220.452
2vz0D64Pteridine reductase/0.452
2w3vTOPDihydrofolate reductase/0.452
3srsM23Dihydrofolate reductase1.5.1.30.452
1kl2FONSerine hydroxymethyltransferase/0.451
1m7aMQUDihydrofolate reductase1.5.1.30.451
1rx6DDFDihydrofolate reductase1.5.1.30.451
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.451
3blrCPBCyclin-dependent kinase 92.7.11.220.451
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4mryCEIObelin/0.451
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.451
1s3yTQTDihydrofolate reductase1.5.1.30.450
2e9uA25Serine/threonine-protein kinase Chk12.7.11.10.450
2f2cAP9Cyclin-dependent kinase 62.7.11.220.450
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.450
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3lanKBTGag-Pol polyprotein2.7.7.490.450
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
1rk3VDXVitamin D3 receptor/0.449
1rkhVD2Vitamin D3 receptor/0.449
2fzjDH3Dihydrofolate reductase1.5.1.30.449
2zv2609Calcium/calmodulin-dependent protein kinase kinase 22.7.11.170.449
3h18PMSEsterase/lipase/0.449
4eok4SPCyclin-dependent kinase 22.7.11.220.449
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
1f4gTP4Thymidylate synthase/0.448
1oguST8Cyclin-dependent kinase 22.7.11.220.448
1tdcUMPThymidylate synthase/0.448
2iw84SPCyclin-dependent kinase 22.7.11.220.448
2j8zNAPQuinone oxidoreductase PIG310.448
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.448
3pd3A3TThreonine--tRNA ligase6.1.1.30.448
3rkb12ZCyclin-dependent kinase 22.7.11.220.448
3sruQ26Dihydrofolate reductase1.5.1.30.448
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.448
4lsjLSJGlucocorticoid receptor/0.448
4mm9FVXNa(+):neurotransmitter symporter (Snf family)/0.448
1al8DHPPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.447
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
2hb8MVDVitamin D3 receptor/0.447
2uzeC95Cyclin-dependent kinase 22.7.11.220.447
3nr4PYVAbscisic acid receptor PYL2/0.447
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
3vrvYSDVitamin D3 receptor/0.447
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
2wcgMT5Glucosylceramidase3.2.1.450.446
2x7gPVBSRSF protein kinase 22.7.11.10.446
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.446
3i64DNA2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase/0.446
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.446
4fi1ATPCasein kinase II subunit alpha2.7.11.10.446
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4h9614QDihydrofolate reductase1.5.1.30.446
4h9814QUncharacterized protein/0.446
1xuzMMNCapsule biosynthesis protein/0.445
1y91CT9Cyclin-dependent kinase 22.7.11.220.445
2wouZZFTGF-beta receptor type-12.7.11.300.445
2ycwCAUBeta-1 adrenergic receptor/0.445
3ezrEZRCyclin-dependent kinase 22.7.11.220.445
3sqq99ZCyclin-dependent kinase 22.7.11.220.445
4g210VPVitamin D3 receptor A/0.445
4iaq2GM5-hydroxytryptamine receptor 1B/0.445
4mmc29JNa(+):neurotransmitter symporter (Snf family)/0.445
4rupH97Vitamin D3 receptor A/0.445
1dduCB3Thymidylate synthase/0.444
3h3sH15Collagen type IV alpha-3-binding protein/0.444
3sai9DRDihydrofolate reductase/0.444
3vt3VDXVitamin D3 receptor/0.444
3vtbTKAVitamin D3 receptor/0.444
4eoi1ROCyclin-dependent kinase 22.7.11.220.444
5k2cZMAAdenosine receptor A2a/0.444
1rf7DHFDihydrofolate reductase1.5.1.30.443
2b55D31Cyclin-dependent kinase 22.7.11.220.443
2broDF2Serine/threonine-protein kinase Chk12.7.11.10.443
2c6tDT5Cyclin-dependent kinase 22.7.11.220.443
2w3wVG9Dihydrofolate reductase/0.443
2wgjVGHHepatocyte growth factor receptor2.7.10.10.443
3gphOIDCytochrome P450 2E11.14.130.443
3i8aN22Dihydrofolate reductase1.5.1.30.443
3qg2CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.443
3vtcTK3Vitamin D3 receptor/0.443
4f700STCyclin-dependent kinase 82.7.11.220.443
4ia7BIVVitamin D3 receptor A/0.443
4j6cSTRCytochrome P450 monooxygenase/0.443
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.443
1hfqMOTDihydrofolate reductase1.5.1.30.442
1ludTRRDihydrofolate reductase1.5.1.30.442
1s19MC9Vitamin D3 receptor/0.442
1s9qOHTEstrogen-related receptor gamma/0.442
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.442
2cchATPCyclin-dependent kinase 22.7.11.220.442
2e9oA58Serine/threonine-protein kinase Chk12.7.11.10.442
2g1pSAHDNA adenine methylase2.1.1.720.442
3qziX72Cyclin-dependent kinase 22.7.11.220.442
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
4mm48PRNa(+):neurotransmitter symporter (Snf family)/0.442
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.442
1cqp803Integrin alpha-L/0.441
1db1VDXVitamin D3 receptor/0.441
1fkoEFZGag-Pol polyprotein2.7.7.490.441
1kt3RTLRetinol-binding protein 4/0.441
1o5rFR9Adenosine deaminase3.5.4.40.441
1v0oINRCell division control protein 2 homolog2.7.11.220.441
1vjy460TGF-beta receptor type-12.7.11.300.441
1xwsBI1Serine/threonine-protein kinase pim-12.7.11.10.441
2bjuIH4Plasmepsin-23.4.23.390.441
2e9p77ASerine/threonine-protein kinase Chk12.7.11.10.441
2hcdBIVVitamin D3 receptor A/0.441
2i0ePDSProtein kinase C beta type2.7.11.130.441
2zb45OPProstaglandin reductase 21.3.1.480.441
2zjwREFCasein kinase II subunit alpha2.7.11.10.441
3a60STURibosomal protein S6 kinase beta-12.7.11.10.441
3d84NDPDihydrofolate reductase1.5.1.30.441
3h3t16HCollagen type IV alpha-3-binding protein/0.441
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.441
3rmeRMEAcidic mammalian chitinase3.2.1.140.441
4aoi4K0Hepatocyte growth factor receptor2.7.10.10.441
4gfg0XFTyrosine-protein kinase SYK2.7.10.20.441
4jzr4JREgl nine homolog 1/0.441
3qakUKAAdenosine receptor A2a/0.441
1kqwRTLCellular retinol-binding protein type II/0.440
1v79FR7Adenosine deaminase3.5.4.40.440
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.440
2iw6QQ2Cyclin-dependent kinase 22.7.11.220.440
3bgpVX1Serine/threonine-protein kinase pim-12.7.11.10.440
3dg8RJ6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
3gc9B45Mitogen-activated protein kinase 112.7.11.240.440
3pqbVGPPutative oxidoreductase/0.440
3qrtX14Cyclin-dependent kinase 22.7.11.220.440
3sa27DRDihydrofolate reductase/0.440
4anmWULCasein kinase II subunit alpha2.7.11.10.440
4fhi0S4Vitamin D3 receptor A/0.440
4g20484Vitamin D3 receptor A/0.440
4ugaQ05Nitric oxide synthase oxygenase1.14.13.1650.440