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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
3datMTXDihydrofolate reductase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3datMTXDihydrofolate reductase/1.000
2zzaFOLDihydrofolate reductase/0.579
3ia4MTXDihydrofolate reductase/0.571
4ele31IDihydrofolate reductase/0.571
3sa16DRDihydrofolate reductase/0.570
3fl8RARDihydrofolate reductase/0.565
3frfXCFDihydrofolate reductase1.5.1.30.556
4nx6FOLDihydrofolate reductase1.5.1.30.551
4elb34SDihydrofolate reductase/0.549
3sa27DRDihydrofolate reductase/0.548
1rx3MTXDihydrofolate reductase1.5.1.30.545
4fgh0U6Dihydrofolate reductase1.5.1.30.543
3frdDHFDihydrofolate reductase1.5.1.30.542
3sruQ26Dihydrofolate reductase1.5.1.30.539
3srwQ27Dihydrofolate reductase1.5.1.30.537
2cd2FOLDihydrofolate reductase1.5.1.30.535
4fgg0U5Dihydrofolate reductase1.5.1.30.533
4nx7FOLDihydrofolate reductase1.5.1.30.532
3fywXCFDihydrofolate reductase1.5.1.30.531
1cd2FOLDihydrofolate reductase1.5.1.30.529
1draMTXDihydrofolate reductase1.5.1.30.529
2fzhDH1Dihydrofolate reductase1.5.1.30.529
3sai9DRDihydrofolate reductase/0.529
2drcMTXDihydrofolate reductase1.5.1.30.528
4elf35IDihydrofolate reductase/0.528
4xe606UDihydrofolate reductase1.5.1.30.526
3jw5TOPDihydrofolate reductase/0.525
3m08RARDihydrofolate reductase1.5.1.30.524
4elg52JDihydrofolate reductase/0.523
3cseN22Uncharacterized protein/0.522
1rg7MTXDihydrofolate reductase1.5.1.30.521
3cd2MTXDihydrofolate reductase1.5.1.30.521
3dauMTXDihydrofolate reductase1.5.1.30.521
3freTOPDihydrofolate reductase1.5.1.30.521
3dfrMTXDihydrofolate reductase1.5.1.30.520
3jwcEKBDihydrofolate reductase/0.518
3srrQ20Dihydrofolate reductase1.5.1.30.518
3ix9MTXDihydrofolate reductase1.5.1.30.516
1dajMOTDihydrofolate reductase1.5.1.30.515
1drbMTXDihydrofolate reductase1.5.1.30.514
1tdrMTXDihydrofolate reductase1.5.1.30.514
3fy9XCFDihydrofolate reductase1.5.1.30.512
3fyvXCFDihydrofolate reductase1.5.1.30.512
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.511
1j3kWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.510
3srsM23Dihydrofolate reductase1.5.1.30.504
1rc4DDFDihydrofolate reductase1.5.1.30.503
1vj3TABDihydrofolate reductase1.5.1.30.503
2w9gTOPDihydrofolate reductase1.5.1.30.503
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.502
3tq9MTXDihydrofolate reductase/0.502
4elh53IDihydrofolate reductase/0.502
3srqQ19Dihydrofolate reductase1.5.1.30.501
4ixgIXGDihydrofolate reductase1.5.1.30.501
1jolFFODihydrofolate reductase1.5.1.30.500
4x5gFOLDihydrofolate reductase1.5.1.30.500
4dfrMTXDihydrofolate reductase1.5.1.30.498
2puiADPMethylthioribose kinase2.7.1.1000.496
2qk8MTXDihydrofolate reductase/0.496
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.496
3fl9TOPDihydrofolate reductase/0.494
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.494
3tqbFOLDihydrofolate reductase/0.494
4ixfIXFDihydrofolate reductase1.5.1.30.494
1ddrMTXDihydrofolate reductase1.5.1.30.493
3ft8MOJHeat shock protein HSP 90-alpha/0.493
3invC50Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.493
3qly55VUncharacterized protein/0.493
4elb34RDihydrofolate reductase/0.493
4h9814QUncharacterized protein/0.493
3qgtCP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.492
1qzfFOLBifunctional dihydrofolate reductase-thymidylate synthase/0.491
1ddsMTXDihydrofolate reductase1.5.1.30.489
1ly3COGDihydrofolate reductase1.5.1.30.489
3qg2CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.489
1re7FOLDihydrofolate reductase1.5.1.30.488
4x5fFOLDihydrofolate reductase1.5.1.30.488
3td8D2RDihydrofolate reductase1.5.1.30.487
1e26GPBDihydrofolate reductase1.5.1.30.486
2excJNKMitogen-activated protein kinase 102.7.11.240.486
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.486
3eej53RUncharacterized protein/0.485
3fy8XCFDihydrofolate reductase1.5.1.30.485
5hi6MTXDihydrofolate reductase/0.484
1cm8ANPMitogen-activated protein kinase 12/0.483
2fziDH3Dihydrofolate reductase1.5.1.30.483
2pmlANPUncharacterized protein/0.482
2pupADPMethylthioribose kinase2.7.1.1000.482
2w3vTOPDihydrofolate reductase/0.482
1x2hLPALipoate-protein ligase A6.3.1.200.481
2pulACPMethylthioribose kinase2.7.1.1000.479
3eem53VUncharacterized protein/0.479
3fraI2HDihydrofolate reductase1.5.1.30.479
3sgy06WDihydrofolate reductase1.5.1.30.479
3wowANPCasein kinase II subunit alpha2.7.11.10.479
4gvjADPNon-receptor tyrosine-protein kinase TYK22.7.10.20.479
4ixeIXEDihydrofolate reductase1.5.1.30.479
1dg5TOPDihydrofolate reductase1.5.1.30.478
1kmvLIIDihydrofolate reductase1.5.1.30.478
4dp3MMVBifunctional dihydrofolate reductase-thymidylate synthase/0.478
3jsuKA5Bifunctional dihydrofolate reductase-thymidylate synthase/0.477
3sh25DRDihydrofolate reductase1.5.1.30.477
4yekTHMThymidine phosphorylase/0.477
3clbTMQBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.476
3jw3TOPDihydrofolate reductase/0.476
1j3iWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.475
2pywADPMethylthioribose kinase2.7.1.1000.475
3k5uPFQAurora kinase A2.7.11.10.475
3qlxQLRUncharacterized protein/0.474
1rb3MTXDihydrofolate reductase1.5.1.30.473
2blaCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.473
2c6eHPMAurora kinase A2.7.11.10.473
3pffADPATP-citrate synthase2.3.3.80.473
3dgaRJ1Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.472
4kjjFOLDihydrofolate reductase1.5.1.30.472
1diuBDMDihydrofolate reductase1.5.1.30.471
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.471
2hm9TRRDihydrofolate reductase1.5.1.30.471
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.471
4m6l21VDihydrofolate reductase1.5.1.30.470
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.469
4jlj1NMDeoxycytidine kinase2.7.1.740.469
4yswFADXanthine dehydrogenase/oxidase/0.469
2b9fADPMitogen-activated protein kinase FUS32.7.11.240.468
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.468
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.468
4cd2FOLDihydrofolate reductase1.5.1.30.468
1ie4T44Transthyretin/0.467
3eek53SUncharacterized protein/0.467
4y12AGSSerine/threonine-protein kinase PknG2.7.11.10.467
2a4zBYMPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.466
2henADPEphrin type-B receptor 22.7.10.10.466
3l8p0CEAngiopoietin-1 receptor2.7.10.10.466
3qlzQLZUncharacterized protein/0.466
1dg7WRBDihydrofolate reductase1.5.1.30.465
3f69XDRSerine/threonine-protein kinase PknB2.7.11.10.465
3orlAGSSerine/threonine protein kinase/0.465
4r1lADPPhenylacetate-coenzyme A ligase/0.465
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.464
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.464
2q5oTPWIndole-3-pyruvate decarboxylase4.1.1.740.464
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.464
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
4m2xTMQDihydrofolate reductase1.5.1.30.464
1df7MTXDihydrofolate reductase1.5.1.30.463
2bfyH1NAurora kinase B-A2.7.11.10.463
3jwm5WBDihydrofolate reductase/0.463
3rpr25ZCyclin-dependent kinase 22.7.11.220.463
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.463
4awiAQ2Mitogen-activated protein kinase 82.7.11.240.463
1lp4ANPCasein kinase II subunit alpha2.7.11.10.462
4fl3ANPTyrosine-protein kinase SYK2.7.10.20.462
4qmlANPSerine/threonine-protein kinase 242.7.11.10.462
1ykdCMPAdenylate cyclase/0.461
2bbqPFGThymidylate synthase/0.461
1rx8FOLDihydrofolate reductase1.5.1.30.460
3t8oATPRhodopsin kinase/0.460
4fl2ANPTyrosine-protein kinase SYK2.7.10.20.460
1u54ACPActivated CDC42 kinase 1/0.459
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.459
1b38ATPCyclin-dependent kinase 22.7.11.220.458
1hfpMOTDihydrofolate reductase1.5.1.30.458
1kmsLIHDihydrofolate reductase1.5.1.30.458
2izrBRKCasein kinase I isoform gamma-32.7.11.10.458
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
1iidNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.457
2vwu7X1Ephrin type-B receptor 42.7.10.10.457
2zdt46CMitogen-activated protein kinase 102.7.11.240.457
3eel53TUncharacterized protein/0.457
3eigMTXDihydrofolate reductase1.5.1.30.457
3um81CYBifunctional dihydrofolate reductase-thymidylate synthase/0.457
4dphP65Bifunctional dihydrofolate reductase-thymidylate synthase/0.457
1hfqMOTDihydrofolate reductase1.5.1.30.456
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.456
5iqiGNPBifunctional AAC/APH2.3.10.456
2q5oPPYIndole-3-pyruvate decarboxylase4.1.1.740.455
3ttjJBIMitogen-activated protein kinase 102.7.11.240.455
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.455
4fuyEK2Mitogen-activated protein kinase 12.7.11.240.455
2cig1DGDihydrofolate reductase1.5.1.30.454
2w1fL0FAurora kinase A2.7.11.10.454
3ql3FOLDihydrofolate reductase1.5.1.30.454
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.454
4e37NDPCatalase1.11.1.60.454
4lvg20ONicotinamide phosphoribosyltransferase2.4.2.120.454
4o1pANPRibonuclease L/0.454
1ir3ANPInsulin receptor2.7.10.10.453
2zva1N1Tyrosine-protein kinase Lyn2.7.10.20.453
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.453
3mqe416Prostaglandin G/H synthase 21.14.99.10.453
4eor4SPCyclin-dependent kinase 22.7.11.220.453
4iayADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
5e92ANPTGF-beta receptor type-22.7.11.300.453
1s3yTQTDihydrofolate reductase1.5.1.30.452
2qocANPEphrin type-A receptor 32.7.10.10.452
3gu5ANPDeath-associated protein kinase 12.7.11.10.452
3oriAGSSerine/threonine protein kinase/0.452
3r0tFU9Casein kinase II subunit alpha2.7.11.10.452
4c58824Cyclin-G-associated kinase2.7.11.10.452
4wujFMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy/0.452
4y0xADPSerine/threonine-protein kinase PknG2.7.11.10.452
4zohFADPutative oxidoreductase FAD-binding subunit/0.452
5l8lADPAurora kinase A2.7.11.10.452
1tz8DESTransthyretin/0.451
2punACPMethylthioribose kinase2.7.1.1000.451
2xizXIZSerine/threonine-protein kinase pim-12.7.11.10.451
3bi6396Wee1-like protein kinase2.7.10.20.451
3och2MXDihydrofolate reductase1.5.1.30.451
4bb3KKAIsopenicillin N synthase1.21.3.10.451
4jrnANPRhoptry kinase family protein/0.451
4x2dATPFic family protein putative filamentation induced by cAMP protein/0.451
5awmANPStress-activated protein kinase JNK2.7.11.240.451
1aoeGW3Dihydrofolate reductase1.5.1.30.450
1ia1TQ3Dihydrofolate reductase1.5.1.30.450
1l8qADPChromosomal replication initiator protein DnaA/0.450
1m78CLZDihydrofolate reductase1.5.1.30.450
4hni16WCasein kinase I isoform epsilon2.7.11.10.450
4xx9ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.450
1ci7UMPThymidylate synthase2.1.1.450.449
1dayGNPCasein kinase II subunit alpha2.7.11.10.449
1f8rFADL-amino-acid oxidase1.4.3.20.449
2e1mFADL-glutamate oxidase/0.449
3ormAGSSerine/threonine protein kinase/0.449
3repATPIntegrin-linked protein kinase2.7.11.10.449
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4gmy0X5Tyrosine-protein kinase JAK2/0.449
4jlk1NODeoxycytidine kinase2.7.1.740.449
4m7vRARDihydrofolate reductase/0.449
1rf7DHFDihydrofolate reductase1.5.1.30.448
2pg0FADAcyl-CoA dehydrogenase/0.448
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.448
2yk2YJWHeat shock protein HSP 90-alpha/0.448
3b8r887Vascular endothelial growth factor receptor 22.7.10.10.448
3hkoANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands/0.448
3l3rOAGDihydrofolate reductase1.5.1.30.448
3ortAGSSerine/threonine protein kinase/0.448
3s1cZIRCytokinin dehydrogenase 11.5.99.120.448
4l9kEHFSerum albumin/0.448
5dosATPAurora kinase A2.7.11.10.448
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.447
1q8yADPSerine/threonine-protein kinase SKY12.7.11.10.447
1q97ATPSerine/threonine-protein kinase SKY12.7.11.10.447
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.447
3v9v21LPeroxisome proliferator-activated receptor gamma/0.447
4bfmANPMaternal embryonic leucine zipper kinase2.7.11.10.447
4ckcSAHmRNA-capping enzyme catalytic subunit2.1.1.560.447
4h2nFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.447
5cvhADPCasein kinase II subunit alpha2.7.11.10.447
1bozPRDDihydrofolate reductase1.5.1.30.446
1rbyKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.446
1rc1KT3Trifunctional purine biosynthetic protein adenosine-32.1.2.20.446
1xjjDGTVitamin B12-dependent ribonucleotide reductase/0.446
3dpd41APhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
3qls55VDihydrofolate reductase1.5.1.30.446
3zonIK1Non-receptor tyrosine-protein kinase TYK22.7.10.20.446
4h9753SDihydrofolate reductase1.5.1.30.446
5auwQUEDeath-associated protein kinase 12.7.11.10.446
1x8b824Wee1-like protein kinase2.7.10.20.445
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.445
2dcnADP2-keto-3-deoxy-gluconate kinase/0.445
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.445
3m09RARDihydrofolate reductase1.5.1.30.445
3qyoQ24Dihydrofolate reductase1.5.1.30.445
3w16P9JAurora kinase A2.7.11.10.445
4bl1ANPMaternal embryonic leucine zipper kinase2.7.11.10.445
4hyu1BKMitogen-activated protein kinase 82.7.11.240.445
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.445
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
1ia3TQ5Dihydrofolate reductase1.5.1.30.444
1klkPMDDihydrofolate reductase1.5.1.30.444
1y4lSVRBasic phospholipase A2 homolog 2/0.444
2fpcSCGStrictosidine synthase4.3.3.20.444
2qoqANPEphrin type-A receptor 32.7.10.10.444
2vd0D27Hematopoietic prostaglandin D synthase/0.444
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.444
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.444
3c4zADPRhodopsin kinase/0.444
3icsCOACoenzyme A disulfide reductase/0.444
3lu8IQXSerum albumin/0.444
3orkAGSSerine/threonine protein kinase/0.444
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.444
3vthAPCCarbamoyltransferase/0.444
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.444
4z34ON7Lysophosphatidic acid receptor 1/0.444
1ckpPVBCyclin-dependent kinase 22.7.11.220.443
2blbCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.443
2hy81STSerine/threonine-protein kinase PAK 12.7.11.10.443
2ptfFMNUncharacterized protein MTH_863/0.443
2qg2A91Heat shock protein HSP 90-alpha/0.443
2qo9ANPEphrin type-A receptor 32.7.10.10.443
3gieACPSensor histidine kinase DesK2.7.13.30.443
4em9TCEPeroxisome proliferator-activated receptor gamma/0.443
4riyANPReceptor tyrosine-protein kinase erbB-32.7.10.10.443
5d4vSAHUncharacterized protein MJ0489/0.443
1a72PADAlcohol dehydrogenase E chain1.1.1.10.442
1dawANPCasein kinase II subunit alpha2.7.11.10.442
2b1pAIZMitogen-activated protein kinase 102.7.11.240.442
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.442
2wotZZGTGF-beta receptor type-12.7.11.300.442
3cs8BRLPeroxisome proliferator-activated receptor gamma/0.442
3gxlQIGTGF-beta receptor type-12.7.11.300.442
3orpAGSSerine/threonine protein kinase/0.442
3pjtC2EDiguanylate cyclase/phosphodiesterase/0.442
3qtsX46Cyclin-dependent kinase 22.7.11.220.442
3t3r9PLCytochrome P450 2A61.14.130.442
4aotGW8Serine/threonine-protein kinase 102.7.11.10.442
4nm0ADPGlycogen synthase kinase-3 beta2.7.11.260.442
4nmbFADBifunctional protein PutA/0.442
1uu9BI33-phosphoinositide-dependent protein kinase 12.7.11.10.441
2bx8AZQSerum albumin/0.441
2np8CC3Aurora kinase A2.7.11.10.441
2o2u738Mitogen-activated protein kinase 102.7.11.240.441
2o65MYFSerine/threonine-protein kinase pim-12.7.11.10.441
3dh7FMNIsopentenyl-diphosphate delta-isomerase/0.441
3efwAK8Aurora kinase A2.7.11.10.441
3igoANPCalmodulin-domain protein kinase 1, putative/0.441
3oroAGSSerine/threonine protein kinase/0.441
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.441
4g8zTOPDihydrofolate reductase1.5.1.30.441
4qysPLRTryptophan synthase beta chain 24.2.1.200.441
1b39ATPCyclin-dependent kinase 22.7.11.220.440
1ht834CProstaglandin G/H synthase 11.14.99.10.440
2bdjHETProto-oncogene tyrosine-protein kinase Src2.7.10.20.440
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.440
2x4f16XMyosin light chain kinase family member 42.7.11.10.440
3ddpRC8Cyclin-dependent kinase 22.7.11.220.440
3ln1CELProstaglandin G/H synthase 21.14.99.10.440
3mtfA3FActivin receptor type-12.7.11.300.440
3nga3NGCasein kinase II subunit alpha2.7.11.10.440
4bi0Z0WDual specificity protein kinase TTK2.7.12.10.440
4n57ADPAPH(2'')-Id/0.440
4ryvZEAProtein LlR18A/0.440