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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
1brpRTLRetinol-binding protein 4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1brpRTLRetinol-binding protein 4/1.000
1iiuRTLRetinol-binding protein 4/0.645
1kt7RTLRetinol-binding protein 4/0.630
1aqbRTLRetinol-binding protein 4/0.627
1felFENRetinol-binding protein 4/0.622
1kt3RTLRetinol-binding protein 4/0.621
1kt4RTLRetinol-binding protein 4/0.616
1kt6RTLRetinol-binding protein 4/0.610
3fmz2T1Retinol-binding protein 4/0.535
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.488
3toxNAPPutative oxidoreductase/0.486
4iui1GQEstrogen receptor/0.478
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.475
4j6cSTRCytochrome P450 monooxygenase/0.474
2wonZZEGag-Pol polyprotein2.7.7.490.473
5fm7ADPRuvB-like helicase/0.472
1ot7CHCBile acid receptor/0.470
3oafOAGDihydrofolate reductase1.5.1.30.470
5jtbZMAAdenosine receptor A2a/0.469
1thnADPAnti-sigma F factor/0.467
3bfa9ODOdorant binding protein ASP1/0.467
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.467
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.467
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.467
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.467
1tvrTB9Gag-Pol polyprotein2.7.7.490.465
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.465
3c3dFO12-phospho-L-lactate transferase/0.465
4c77N01Phenylacetone monooxygenase1.14.13.920.465
5jlaNADPutative short-chain dehydrogenase/reductase/0.465
2iltNN1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.464
3angDCCTranscriptional repressor, TetR family/0.464
5eccNAPDehydrofolate reductase type I/0.464
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.463
1upw444Oxysterols receptor LXR-beta/0.463
2aylFLPProstaglandin G/H synthase 11.14.99.10.463
3dlgGWEGag-Pol polyprotein2.7.7.490.463
3qm4PN0Cytochrome P450 2D6/0.463
4ez8DHFThymidylate synthase2.1.1.450.463
4lb2DM5Serum albumin/0.463
1fcx184Retinoic acid receptor gamma/0.462
1w4zNAPPutative ketoacyl reductase1.3.10.462
2fonFADAcyl-coenzyme A oxidase/0.462
3iptEQUSteroid Delta-isomerase5.3.3.10.462
3qlsNDPDihydrofolate reductase1.5.1.30.462
4h4o506Gag-Pol polyprotein2.7.7.490.462
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.461
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.461
2jn3JN3Fatty acid-binding protein, liver/0.460
2xvv9DNSerum albumin/0.460
3ictADPCoenzyme A disulfide reductase/0.460
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
4m10ICDProstaglandin G/H synthase 21.14.99.10.459
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.458
1rx7FOLDihydrofolate reductase1.5.1.30.458
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.458
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
3w5p4OAVitamin D3 receptor/0.458
4hyf1AKTankyrase-22.4.2.300.458
4pd6URINucleoside permease/0.458
5k2dZMAAdenosine receptor A2a/0.458
1ai9NDPDihydrofolate reductase1.5.1.30.457
2y5dNAP3,4-dehydroadipyl-CoA semialdehyde dehydrogenase/0.457
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.457
3u8hBHPPhospholipase A2, membrane associated/0.457
5ikrID8Prostaglandin G/H synthase 21.14.99.10.457
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.456
2ociTYCValacyclovir hydrolase3.10.456
3gwfFADCyclohexanone monooxygenase/0.456
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.456
3irxUDRGag-Pol polyprotein2.7.7.490.456
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.456
4l8u9AZSerum albumin/0.456
5k2bZMAAdenosine receptor A2a/0.456
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.455
2b00GCHPhospholipase A2, major isoenzyme3.1.1.40.455
2q9fC3SCholesterol 24-hydroxylase/0.455
3a1l2CCCytochrome P450/0.455
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.455
3c6tM14Gag-Pol polyprotein2.7.7.490.455
3vt7VDXVitamin D3 receptor/0.455
3vtdTKDVitamin D3 receptor/0.455
4bb3KKAIsopenicillin N synthase1.21.3.10.455
4i9i1DYTankyrase-12.4.2.300.455
4xbfFADLysine-specific histone demethylase 1A10.455
1osvCHCBile acid receptor/0.454
1rd4L08Integrin alpha-L/0.454
1xdkREARetinoic acid receptor beta/0.454
2be2R22Gag-Pol polyprotein2.7.7.490.454
2w98P1ZProstaglandin reductase 21.3.1.480.454
2ydvNECAdenosine receptor A2a/0.454
3c3eGDP2-phospho-L-lactate transferase/0.454
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
3lalKRVGag-Pol polyprotein2.7.7.490.454
3q7dNPXProstaglandin G/H synthase 21.14.99.10.454
3vt5YI2Vitamin D3 receptor/0.454
4eoi1ROCyclin-dependent kinase 22.7.11.220.454
4g95OAGDihydrofolate reductase1.5.1.30.454
4iaq2GM5-hydroxytryptamine receptor 1B/0.454
1qnfHDFDeoxyribodipyrimidine photo-lyase4.1.99.30.453
2zevIPEGeranylgeranyl pyrophosphate synthase/0.453
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.453
4dbs0HVAldo-keto reductase family 1 member C3/0.453
5k2aZMAAdenosine receptor A2a/0.453
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
2qd5CHDFerrochelatase, mitochondrial4.99.1.10.452
2y05NAPProstaglandin reductase 1/0.452
1w06W05Isopenicillin N synthase1.21.3.10.451
2b1i93ABifunctional purine biosynthesis protein PURH2.1.2.30.451
2hnzPC0Gag-Pol polyprotein2.7.7.490.451
2z4y252Geranylgeranyl pyrophosphate synthase/0.451
3eq6BCOAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.451
3qlrNDPDihydrofolate reductase1.5.1.30.451
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.451
1al7HSTPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.450
1fd0254Retinoic acid receptor gamma/0.450
1kt5RTLRetinol-binding protein 4/0.450
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.450
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.450
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
1x7hNDPPutative ketoacyl reductase1.3.10.449
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.449
2z78H86Geranylgeranyl pyrophosphate synthase/0.449
3bzuA21Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3t1a5MAGag-Pol polyprotein2.7.7.490.449
3tm5SFGUncharacterized protein/0.449
2wd8VGFPteridine reductase/0.448
2zb8IMNProstaglandin reductase 21.3.1.480.448
3d75NBBPheromone-binding protein ASP1/0.448
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.448
4dvi2IWTankyrase-12.4.2.300.448
3emlZMAAdenosine receptor A2a/0.448
1dr3HBIDihydrofolate reductase1.5.1.30.447
1jq5NADGlycerol dehydrogenase1.1.1.60.447
1m52P17Tyrosine-protein kinase ABL12.7.10.20.447
2r0pK2CPutative FAD-monooxygenase/0.447
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3d84NDPDihydrofolate reductase1.5.1.30.447
3drpR8EGag-Pol polyprotein2.7.7.490.447
3w0hW12Vitamin D3 receptor/0.447
4bj9UHBTankyrase-22.4.2.300.447
4kl9NDPDihydrofolate reductase1.5.1.30.447
5k2cZMAAdenosine receptor A2a/0.447
1lriCLRBeta-elicitin cryptogein/0.446
1n83CLRNuclear receptor ROR-alpha/0.446
1x7gNAPPutative ketoacyl reductase1.3.10.446
1xddAAYIntegrin alpha-L/0.446
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.446
3mg3ECHOrange carotenoid-binding protein/0.446
3nwlNDPCatalase1.11.1.60.446
3pghFLPProstaglandin G/H synthase 21.14.99.10.446
4b5pACOAlpha-tubulin N-acetyltransferase 1/0.446
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.446
4fm5DF0Prostaglandin G/H synthase 21.14.99.10.446
1c7oPPGHemolysin/0.445
2ydoADNAdenosine receptor A2a/0.445
2ykbYKBHeat shock protein HSP 90-alpha/0.445
3gkjHC3Niemann-Pick C1 protein/0.445
3is9AC7Gag-Pol polyprotein2.7.7.490.445
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
4a32MYAGlycylpeptide N-tetradecanoyltransferase/0.445
4a51DQ8Kinesin-like protein KIF11/0.445
4j6bPLOCytochrome P450 monooxygenase/0.445
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.445
1ao8MTXDihydrofolate reductase1.5.1.30.444
1r2jFADFkbI/0.444
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.444
1tilATPAnti-sigma F factor/0.444
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.444
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2yltNAPPhenylacetone monooxygenase1.14.13.920.444
3bfb9ODPheromone-binding protein ASP1/0.444
3eej53RUncharacterized protein/0.444
3lamKRPGag-Pol polyprotein2.7.7.490.444
3s7a684Dihydrofolate reductase1.5.1.30.444
3zeiAWHO-acetylserine sulfhydrylase/0.444
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.444
5iua6DXAdenosine receptor A2a/0.444
4ug2NGIAdenosine receptor A2a/0.444
1dr3TAPDihydrofolate reductase1.5.1.30.443
1dv2ATPBiotin carboxylase6.3.4.140.443
1rf7DHFDihydrofolate reductase1.5.1.30.443
1td2PXLPyridoxal kinase PdxY/0.443
1uyfPU1Heat shock protein HSP 90-alpha/0.443
1w22NHBHistone deacetylase 83.5.1.980.443
2zynBCDPeriplasmic binding protein/0.443
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3uyk0CXProbable NDP-rhamnosyltransferase/0.443
3znqSS8D-amino-acid oxidase1.4.3.30.443
4eiyZMAAdenosine receptor A2a/0.443
4h4m494Gag-Pol polyprotein2.7.7.490.443
4h9614QDihydrofolate reductase1.5.1.30.443
4l1xNAPAldo-keto reductase family 1 member C2/0.443
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.443
1mvsDTMDihydrofolate reductase1.5.1.30.442
1skgVAL_ALA_PHE_ARG_SERBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.442
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.442
2lf1NDPDihydrofolate reductase1.5.1.30.442
2ynfWHUGag-Pol polyprotein2.7.7.490.442
3new3NEMitogen-activated protein kinase 14/0.442
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.442
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.442
3qlwN22Dihydrofolate reductase1.5.1.30.442
3rr3FLRProstaglandin G/H synthase 21.14.99.10.442
4ejmNAPPutative zinc-binding dehydrogenase/0.442
4fizCUE17beta-hydroxysteroid dehydrogenase/0.442
4hxyNDPPlm1/0.442
4jbtASDCytochrome P450 monooxygenase/0.442
1hb3SCVIsopenicillin N synthase1.21.3.10.441
2z52H23Geranylgeranyl pyrophosphate synthase/0.441
3d80Q22Dihydrofolate reductase1.5.1.30.441
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.441
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.441
3p99LNPLanosterol 14-alpha-demethylase/0.441
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
5a3cNADSIR2 family protein/0.441
1dgbNDPCatalase1.11.1.60.440
1pd9CO4Dihydrofolate reductase1.5.1.30.440
1re7FOLDihydrofolate reductase1.5.1.30.440
1zq5E04Aldo-keto reductase family 1 member C3/0.440
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.440
2ban357Gag-Pol polyprotein2.7.7.490.440
2ftoCB3Thymidylate synthase/0.440
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4bfxZVXPantothenate kinase2.7.1.330.440
4d04FADPhenylacetone monooxygenase1.14.13.920.440
4ia2BIVVitamin D3 receptor A/0.440
4iarERM5-hydroxytryptamine receptor 1B/0.440
4rupH97Vitamin D3 receptor A/0.440