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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
4pzkSAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4pzkSAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase/1.000
4kgnSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.572
4jalSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.516
3nk7SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase/0.502
1xe55FEPlasmepsin-23.4.23.390.496
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.496
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.491
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.487
4xboSAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ2.1.1.2000.487
2ha8SAHProbable methyltransferase TARBP1/0.485
3n4kSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.484
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.483
2cy0NAPShikimate dehydrogenase (NADP(+))/0.483
4a61ANPPlasmid segregation protein ParM/0.483
4q73FADBifunctional protein PutA/0.483
4cnfMTASpoU rRNA methylase/0.479
2daaDCSD-alanine aminotransferase2.6.1.210.478
1mxiSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.476
4k28NADShikimate dehydrogenase family protein/0.476
1ae1NAPTropinone reductase 1/0.473
3bbdSAHRibosomal RNA small subunit methyltransferase Nep12.1.10.473
4r1lADPPhenylacetate-coenzyme A ligase/0.473
2rcyNAPPyrroline-5-carboxylate reductase/0.472
3hk1B64Fatty acid-binding protein, adipocyte/0.471
3vswR31Renin3.4.23.150.471
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.470
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.470
1tj0FADBifunctional protein PutA1.5.5.20.470
3lsiFADPyranose 2-oxidase/0.470
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.470
4xg1LLPDiaminopimelate decarboxylase/0.470
3oijSAHRibosomal RNA small subunit methyltransferase NEP1/0.469
2yy8SAMtRNA (cytidine(56)-2'-O)-methyltransferase/0.468
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.467
3kjm245Cytokinin dehydrogenase 11.5.99.120.467
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.466
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.466
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.465
1nzfUPGDNA beta-glucosyltransferase/0.465
3lqfNADGalactitol dehydrogenase/0.465
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.464
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.464
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.463
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.463
2ikuLIYRenin3.4.23.150.463
2p5fSAHDiphthine synthase/0.463
3atyFMNProstaglandin F2a synthase/0.463
3imgBZ3Pantothenate synthetase6.3.2.10.463
3r3sNADPutative oxidoreductase/0.463
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.463
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.463
2e8hSAHDiphthine synthase/0.462
2gfdRDAEndoplasmin/0.462
2owuSAHDiphthine synthase/0.462
4cngSAHSpoU rRNA methylase/0.462
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.461
1orrNADCDP-paratose 2-epimerase/0.461
2givACOHistone acetyltransferase KAT8/0.461
4jwhSAHtRNA (guanine(9)-N1)-methyltransferase/0.461
2i3gNAPN-acetyl-gamma-glutamyl-phosphate reductase1.2.1.380.460
3vydVYDRenin3.4.23.150.460
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.460
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.459
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.459
2eglSAHDiphthine synthase/0.459
4lb2DM5Serum albumin/0.459
4umxNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.459
1a72PADAlcohol dehydrogenase E chain1.1.1.10.458
1beuIPLTryptophan synthase alpha chain/0.458
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
1u71MXADihydrofolate reductase1.5.1.30.458
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.458
2ed3SAHDiphthine synthase/0.458
2g1n1IGRenin3.4.23.150.458
2g247IGRenin3.4.23.150.458
1h50FMNPentaerythritol tetranitrate reductase/0.457
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.457
3cobADPKinesin heavy chain-like protein/0.457
3mt817TGlycogen phosphorylase, muscle form2.4.1.10.457
1cg4IMOAdenylosuccinate synthetase/0.456
1drhNAPDihydrofolate reductase1.5.1.30.456
1h66RH1NAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.456
2hfuMEVMevalonate kinase/0.456
2oapANPType II secretion system protein (GspE-2)/0.456
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.456
4fdpFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.456
1ddrMTXDihydrofolate reductase1.5.1.30.455
1rfuADPPyridoxal kinase2.7.1.350.455
2c3qGTXGlutathione S-transferase theta-12.5.1.180.455
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.455
3imgBZ2Pantothenate synthetase6.3.2.10.455
3s1dZIRCytokinin dehydrogenase 11.5.99.120.455
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
5d3qGDPDynamin-13.6.5.50.455
2ylrNAPPhenylacetone monooxygenase1.14.13.920.454
3gy0NAPNAD(P)-dependent oxidoreductase/0.454
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.454
1kvkATPMevalonate kinase2.7.1.360.453
1nzdUPGDNA beta-glucosyltransferase/0.453
1y4lSVRBasic phospholipase A2 homolog 2/0.453
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.453
2qblCAMCamphor 5-monooxygenase1.14.15.10.453
4acxS8ZBeta-secretase 13.4.23.460.453
4b4vL34Bifunctional protein FolD/0.453
4giu636Anthranilate phosphoribosyltransferase/0.453
1kfbIGPTryptophan synthase alpha chain/0.452
1lbcCYZGlutamate receptor 2/0.452
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.452
3etgNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.452
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.452
4v2gITCTetracycline repressor protein class D/0.452
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.452
1bil0IURenin3.4.23.150.451
2a7r5GPGMP reductase 2/0.451
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.451
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.451
2qbmCAMCamphor 5-monooxygenase1.14.15.10.451
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.451
3jv7NADSecondary alcohol dehydrogenase/0.451
4dc0NDPPutative ketoacyl reductase1.3.10.451
1e3wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.450
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.450
2rlcCHDCholoylglycine hydrolase3.5.1.240.450
2x0rNADMalate dehydrogenase/0.450
2y05NAPProstaglandin reductase 1/0.450
3pgqGY3Acetyl-CoA carboxylase/0.450
1honGNHAdenylosuccinate synthetase/0.449
1pjcNADAlanine dehydrogenase/0.449
1ra3NAPDihydrofolate reductase1.5.1.30.449
1rneC60Renin3.4.23.150.449
1w6hTITPlasmepsin-23.4.23.390.449
2a94AP0L-lactate dehydrogenase1.1.1.270.449
2gmjFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.449
2vhtATPNTPase P4/0.449
3vt7VDXVitamin D3 receptor/0.449
4lcjNADC-terminal-binding protein 2/0.449
5dp2NAPCurF/0.449
1h51FMNPentaerythritol tetranitrate reductase/0.448
1xelUPGUDP-glucose 4-epimerase5.1.3.20.448
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
2g1o2IGRenin3.4.23.150.448
2hutSAHDiphthine synthase/0.448
2pckSAHDiphthine synthase/0.448
3gwdNAPCyclohexanone monooxygenase/0.448
3r95ACOMccE protein/0.448
3wleNAD(R)-specific carbonyl reductase/0.448
4fue7UPUrokinase-type plasminogen activator3.4.21.730.448
4jwfSAHtRNA (guanine(9)-N1)-methyltransferase/0.448
1h73ANPHomoserine kinase2.7.1.390.447
1p9pSAHtRNA (guanine-N(1)-)-methyltransferase/0.447
2dshSAHDiphthine synthase/0.447
2dv3SAHDiphthine synthase/0.447
3ctyFADProbable thioredoxin reductase/0.447
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.447
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
4tleAGSCircadian clock protein kinase KaiC2.7.11.10.447
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1ualSAHtRNA (guanine-N(1)-)-methyltransferase2.1.1.2280.446
2a1mCAMCamphor 5-monooxygenase1.14.15.10.446
2ejkSAHDiphthine synthase/0.446
2g1s4IGRenin3.4.23.150.446
2ii6C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.446
2y3sTIRTamL/0.446
3clsFADElectron transfer flavoprotein subunit alpha/0.446
3w6hAZMCarbonic anhydrase 14.2.1.10.446
3zeiAWHO-acetylserine sulfhydrylase/0.446
4q71FADBifunctional protein PutA/0.446
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.446
1culFOKAdenylate cyclase type 2/0.445
1culFOKAdenylate cyclase type 5/0.445
1dz8CAMCamphor 5-monooxygenase1.14.15.10.445
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.445
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.445
2owkSAHDiphthine synthase/0.445
3b7kCOAAcyl-coenzyme A thioesterase 123.1.2.10.445
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.445
3hyoADPPyridoxal kinase/0.445
3tjzGNPADP-ribosylation factor 1/0.445
5c41ACPRibokinase/0.445
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.444
1u2yGOXPancreatic alpha-amylase/0.444
1zji2PG2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.444
2jamJ60Calcium/calmodulin-dependent protein kinase type 1G2.7.11.170.444
2pchSAHDiphthine synthase/0.444
2wdzNADGalactitol dehydrogenase/0.444
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
3f03FMNPentaerythritol tetranitrate reductase/0.444
3kb6NADD-lactate dehydrogenase/0.444
3s79ASDAromatase1.14.14.140.444
4i6gFADCryptochrome-2/0.444
4kgkGTPUncharacterized protein/0.444
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.444
4tyqAP5Adenylate kinase/0.444
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1rc1KT3Trifunctional purine biosynthetic protein adenosine-32.1.2.20.443
2a1oCAMCamphor 5-monooxygenase1.14.15.10.443
2abjPLPBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.443
2djxFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.443
2e8qSAHDiphthine synthase/0.443
2emuSAHDiphthine synthase/0.443
2qbuSAHPrecorrin-2 methyltransferase/0.443
3a3bRBFLumazine protein/0.443
3lpjZ75Beta-secretase 13.4.23.460.443
3lsmSFDPyranose 2-oxidase/0.443
3mpt1GKMitogen-activated protein kinase 14/0.443
3uyk0CXProbable NDP-rhamnosyltransferase/0.443
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.443
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.443
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.443
4mokFADPyranose 2-oxidase/0.443
4opiFDAConserved Archaeal protein/0.443
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
1ra3MTXDihydrofolate reductase1.5.1.30.442
1wngSAHDiphthine synthase/0.442
2ejzSAHDiphthine synthase/0.442
2fznFADBifunctional protein PutA1.5.5.20.442
2q46NAPUncharacterized protein At5g02240/0.442
3b6zCO7Enoyl reductase LovC10.442
3bg7FADPyranose 2-oxidase/0.442
3gonANPPhosphomevalonate kinase/0.442
3s87ADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.442
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
1daaPLPD-alanine aminotransferase2.6.1.210.441
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.441
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1jueFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.441
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.441
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.441
1yreCOAUncharacterized protein/0.441
2d29FADAcyl-CoA dehydrogenase/0.441
2r8oT5XTransketolase 1/0.441
2xgoZKDUncharacterized protein/0.441
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.441
3e2sFADBifunctional protein PutA1.5.5.20.441
4cp4CAMCamphor 5-monooxygenase1.14.15.10.441
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.441
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.441
4m83ERYOleandomycin glycosyltransferase2.4.10.441
4yvkSFGtRNA (guanine-N(1)-)-methyltransferase2.1.1.2280.441
1fwkADPHomoserine kinase2.7.1.390.440
1heuNADAlcohol dehydrogenase E chain1.1.1.10.440
1ja0NAPNADPH--cytochrome P450 reductase/0.440
1omoNADAlanine dehydrogenase/0.440
1rq1FADEndoplasmic oxidoreductin-11.8.40.440
2il2LIXRenin3.4.23.150.440
2xhd7T9Glutamate receptor 2/0.440
2znnS44Peroxisome proliferator-activated receptor alpha/0.440
3iqgASN_TRP_ASN_ILECysteine synthase2.5.1.470.440
3p8jFMNPentaerythritol tetranitrate reductase/0.440
3phiNDPShikimate dehydrogenase (NADP(+))/0.440
3uu114BAnthranilate phosphoribosyltransferase/0.440
3vt8YI3Vitamin D3 receptor/0.440
4dh60KNBeta-secretase 13.4.23.460.440
4mlp2CXCryptochrome-2/0.440
4nr42LKCREB-binding protein/0.440
4rlsNAIL-lactate dehydrogenase A chain1.1.1.270.440
4xq9NADHomospermidine synthase2.5.1.440.440