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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
4e1bTXAThreonylcarbamoyl-AMP synthase2.7.7.87

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4e1bTXAThreonylcarbamoyl-AMP synthase2.7.7.871.000
3okxSAMS-adenosyl-L-methionine-binding protein RPA0152/0.519
1kgjFL8Transthyretin/0.502
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.501
3ajeANPThreonylcarbamoyl-AMP synthase2.7.7.870.499
1tz8DESTransthyretin/0.494
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.486
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.483
2pd7FADVivid PAS protein VVD/0.483
4qvtACOAcetyltransferase YpeA2.3.10.483
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.482
4wxlBB2Peptide deformylase/0.482
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.481
2bx8AZQSerum albumin/0.481
4s33ANPMitogen-activated protein kinase 12.7.11.240.481
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.480
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.479
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.479
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.479
3icrCOACoenzyme A disulfide reductase/0.478
1ictT44Transthyretin/0.477
3uwqU5POrotidine 5'-phosphate decarboxylase/0.476
4l9q9TPSerum albumin/0.476
2pg0FADAcyl-CoA dehydrogenase/0.475
3d72FADVivid PAS protein VVD/0.475
4b6cB5UDNA gyrase subunit B/0.475
8catNDPCatalase1.11.1.60.475
1ie4T44Transthyretin/0.474
2yutNAPPutative short-chain oxidoreductase/0.474
3g6wGTPUracil phosphoribosyltransferase2.4.2.90.474
3s79ASDAromatase1.14.14.140.474
3ntdCOAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.471
3ttiKBIMitogen-activated protein kinase 102.7.11.240.471
1ipeNDPTropinone reductase 21.1.1.2360.470
3zep1NXTyrosine-protein kinase JAK32.7.10.20.470
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.469
2x0iNAIMalate dehydrogenase/0.469
2xb5I7TTetracycline repressor protein class D/0.469
2ywwATPAspartate carbamoyltransferase regulatory chain/0.469
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.469
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.469
3x2vATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.469
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.469
3wecAUICytochrome P450/0.468
4bwxAGSPAB-dependent poly(A)-specific ribonuclease subunit pan3/0.468
4k6rATPBifunctional protein GlmU/0.468
1g6cTZPThiamine-phosphate synthase/0.467
1mjhATPUniversal stress protein MJ0577/0.467
2gsdNADFormate dehydrogenase/0.467
2rghFADAlpha-Glycerophosphate Oxidase/0.467
3gwfFADCyclohexanone monooxygenase/0.467
5bsfNADPyrroline-5-carboxylate reductase/0.467
3k5uPFQAurora kinase A2.7.11.10.466
3ojxNAPNADPH--cytochrome P450 reductase/0.466
4i9aNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]/0.466
7catNDPCatalase1.11.1.60.466
2aazCB3Thymidylate synthase2.1.1.450.465
3hjiFADVivid PAS protein VVD/0.464
3rusADPChaperonin/0.464
4e37NDPCatalase1.11.1.60.464
4n9iPCGCatabolite expression activator/0.464
1o6kANPRAC-beta serine/threonine-protein kinase2.7.11.10.463
4aoxFADSteroid monooxygenase/0.463
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.463
5ap57RODual specificity protein kinase TTK2.7.12.10.463
1g6cIFPThiamine-phosphate synthase/0.462
1gjrNAPFerredoxin--NADP reductase1.18.1.20.462
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.462
2r5tANPSerine/threonine-protein kinase Sgk12.7.11.10.462
2ym2NAPPhenylacetone monooxygenase1.14.13.920.462
3hjkFADVivid PAS protein VVD/0.462
3idcANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.462
3zc3NAPFerredoxin--NADP reductase1.18.1.20.462
4ii5ADPCyclin-dependent kinase 22.7.11.220.462
1f20NAPNitric oxide synthase, brain1.14.13.390.461
1ofgNDPGlucose--fructose oxidoreductase1.1.99.280.461
1qaxHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.461
2p33J07Mitogen-activated protein kinase 102.7.11.240.461
3lnmNAPVoltage-gated potassium channel subunit beta-2/0.461
4b8wNAPGDP-L-fucose synthase1.1.1.2710.461
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.461
4zohFADPutative oxidoreductase FAD-binding subunit/0.461
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.460
2q4bNAPUncharacterized protein At5g02240/0.460
5idwNAPShort-chain dehydrogenase/reductase SDR/0.460
1sx4ADP60 kDa chaperonin/0.459
2ay84TBAromatic-amino-acid aminotransferase2.6.1.570.459
2oapANPType II secretion system protein (GspE-2)/0.459
2vqdAP2Biotin carboxylase6.3.4.140.459
3q4zANPSerine/threonine-protein kinase PAK 12.7.11.10.459
3qfrNAPNADPH--cytochrome P450 reductase/0.459
3sjzGNPTranslation initiation factor 2 subunit gamma/0.459
4hvi19STyrosine-protein kinase JAK32.7.10.20.459
4j1tNADNAD/NADP transhydrogenase alpha subunit 1/0.459
2ojj82AMitogen-activated protein kinase 12.7.11.240.458
3adaNADSubunit alpha of sarocosine oxidase/0.458
3n6mGTPGenome polyprotein/0.458
4gt3ATPMitogen-activated protein kinase 12.7.11.240.458
4l8u9AZSerum albumin/0.458
3sufSUEPolyprotein/0.457
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.457
4s32ANPMitogen-activated protein kinase 12.7.11.240.457
2dcnADP2-keto-3-deoxy-gluconate kinase/0.456
3h86AP5Adenylate kinase/0.456
3nt6COAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.456
4jia1K3Tyrosine-protein kinase JAK2/0.456
1g67TZPThiamine-phosphate synthase/0.455
1w78PD8Dihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.455
1wwkNAD307aa long hypothetical phosphoglycerate dehydrogenase/0.455
2ev9NAPShikimate dehydrogenase (NADP(+))/0.455
2wqeADPAurora kinase A2.7.11.10.455
2z6iFMN2-nitropropane dioxygenase/0.455
2zbzVDXVitamin D3 dihydroxylase/0.455
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.455
4f7l0SOCyclin-dependent kinase 82.7.11.220.455
4kfp1R7Nicotinamide phosphoribosyltransferase2.4.2.120.455
3ms421NGlycogen phosphorylase, muscle form2.4.1.10.454
4at9UTPInterleukin enhancer-binding factor 2/0.454
4ekkANPRAC-alpha serine/threonine-protein kinase2.7.11.10.454
4s34ANPMitogen-activated protein kinase 12.7.11.240.454
5kf8ACOPredicted acetyltransferase/0.454
1aj8COACitrate synthase/0.453
1oaaNAPSepiapterin reductase1.1.1.1530.453
2bmbPMMFolic acid synthesis protein FOL1/0.453
2g78REACellular retinoic acid-binding protein 2/0.453
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.453
4tuvCPZCytochrome P450 1191.140.453
5caeCOASuccinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial6.2.1.40.453
5ifyUMPGlucose-1-phosphate thymidylyltransferase/0.453
1kvtUPGUDP-glucose 4-epimerase5.1.3.20.452
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.452
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.452
2vhwNAIAlanine dehydrogenase1.4.1.10.452
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.452
3lq2TDPPyruvate dehydrogenase E1 component1.2.4.10.452
3pjuC2EDiguanylate cyclase/phosphodiesterase/0.452
4ie0PD2Alpha-ketoglutarate-dependent dioxygenase FTO/0.452
4lvg20ONicotinamide phosphoribosyltransferase2.4.2.120.452
4o1pANPRibonuclease L/0.452
4ydqHFGProline--tRNA ligase6.1.1.150.452
1hzzNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.451
1v9aSAHUncharacterized protein/0.451
2bxnIDBSerum albumin/0.451
3cukFADD-amino-acid oxidase1.4.3.30.451
3g8dADPBiotin carboxylase6.3.4.140.451
3k3bADPKinesin-like protein KIF11/0.451
3lpbNVBTyrosine-protein kinase JAK2/0.451
3tx1FADUDP-N-acetylenolpyruvoylglucosamine reductase/0.451
4jbqVX6Aurora kinase A2.7.11.10.451
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.451
1d7aAIRN5-carboxyaminoimidazole ribonucleotide mutase/0.450
1pmn984Mitogen-activated protein kinase 102.7.11.240.450
1qvnFRIInterleukin-2/0.450
2dbrNAPGlyoxylate reductase1.1.1.260.450
2obyNAPQuinone oxidoreductase PIG310.450
2pdtFADVivid PAS protein VVD/0.450
2v92ATP5'-AMP-activated protein kinase subunit gamma-1/0.450
3g8eIS1Nicotinamide phosphoribosyltransferase2.4.2.120.450
3tqhNDPQuinone oxidoreductase/0.450
3x2uATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
4y9qC2EUncharacterized protein/0.450
1m75NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.449
1njfAGSDNA polymerase III subunit tau2.7.7.70.449
2bacFADPutative aminooxidase/0.449
2bsmBSMHeat shock protein HSP 90-alpha/0.449
2bxaC1FSerum albumin/0.449
2yxuATPPyridoxal kinase2.7.1.350.449
3t1tGDPProbable gliding protein mglA/0.449
4do0DZAHistone lysine demethylase PHF81.14.11.270.449
4kgmATPUncharacterized protein/0.449
5c03AGSNon-receptor tyrosine-protein kinase TYK22.7.10.20.449
1hk2T44Serum albumin/0.448
1qmzATPCyclin-dependent kinase 22.7.11.220.448
1ryeNDPGlucose--fructose oxidoreductase1.1.99.280.448
2excJNKMitogen-activated protein kinase 102.7.11.240.448
2w6nOA2Biotin carboxylase6.3.4.140.448
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.448
3lu6IMXSerum albumin/0.448
3mddFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.448
3qftNAPNADPH--cytochrome P450 reductase/0.448
4jtqNAPAldo-keto reductase family 1 member C2/0.448
4xey1N1Tyrosine-protein kinase ABL12.7.10.20.448
4xxgFADCholesterol oxidase1.1.3.60.448
1g4tFTPThiamine-phosphate synthase/0.447
1glbADPGlycerol kinase/0.447
1j39UPGDNA beta-glucosyltransferase/0.447
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.447
3mpaSB2Mitogen-activated protein kinase 14/0.447
3vs2VSBTyrosine-protein kinase HCK2.7.10.20.447
4deeADPAurora kinase A2.7.11.10.447
4iacACPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
4mokFADPyranose 2-oxidase/0.447
4ubuCOASteroid 3-ketoacyl-CoA thiolase/0.447
5ahsCOAAcyl-CoA dehydrogenase/0.447
1kk4ACOStreptogramin A acetyltransferase2.3.10.446
2gu8796cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2j8zNAPQuinone oxidoreductase PIG310.446
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.446
3ad9NADSubunit alpha of sarocosine oxidase/0.446
3elm24FCollagenase 33.4.240.446
3f1kNAPUncharacterized oxidoreductase YciK10.446
3q30D61Squalene synthase2.5.1.210.446
3qe0GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.446
4bi1ZO6Dual specificity protein kinase TTK2.7.12.10.446
4e07ACPPlasmid partitioning protein ParF/0.446
4emyPLPAminotransferase class I and II/0.446
4yswFADXanthine dehydrogenase/oxidase/0.446
5iqiGNPBifunctional AAC/APH2.3.10.446
1daaPLPD-alanine aminotransferase2.6.1.210.445
1i44ACPInsulin receptor2.7.10.10.445
1q1wFADPutidaredoxin reductase1.18.1.50.445
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.445
1t7i017Gag-Pol polyprotein3.4.23.160.445
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.445
2oj9BMIInsulin-like growth factor 1 receptor2.7.10.10.445
2qr1ADP5'-AMP-activated protein kinase subunit gamma/0.445
2r9eSDXCitrate synthase2.3.3.160.445
2vo6M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
3a7hATPSerine/threonine-protein kinase 242.7.11.10.445
3kb1ADPIron-sulfur cluster carrier protein/0.445
3lu7IPXSerum albumin/0.445
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.445
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.445
3och2MXDihydrofolate reductase1.5.1.30.445
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.445
4c4iX20Dual specificity protein kinase TTK2.7.12.10.445
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.445
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.445
1rj9GCPSignal recognition particle receptor FtsY/0.444
1z7eUGABifunctional polymyxin resistance protein ArnA/0.444
2bpoNAPNADPH--cytochrome P450 reductase/0.444
2c6eHPMAurora kinase A2.7.11.10.444
2cmkCDPCytidylate kinase2.7.4.250.444
2cmvNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.444
2cy0NAPShikimate dehydrogenase (NADP(+))/0.444
2qocANPEphrin type-A receptor 32.7.10.10.444
2y5s78HDihydropteroate synthase/0.444
3frkTQPQdtB/0.444
3h4lANPDNA mismatch repair protein PMS1/0.444
3qe2NAPNADPH--cytochrome P450 reductase/0.444
3r83Z14Cyclin-dependent kinase 22.7.11.220.444
3w8rACPUridine kinase/0.444
4bfsZVSPantothenate kinase2.7.1.330.444
4p2lFADSulfhydryl oxidase 11.8.3.20.444
4wq5ATPtRNA N6-adenosine threonylcarbamoyltransferase/0.444
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
5d3qGDPDynamin-13.6.5.50.444
1jpaANPEphrin type-B receptor 22.7.10.10.443
1ng3FADGlycine oxidase1.4.3.190.443
1nsfATPVesicle-fusing ATPase3.6.4.60.443
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.443
1pn3TYDdTDP-epi-vancosaminyltransferase2.4.1.3110.443
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.443
2hf8GSPProbable hydrogenase nickel incorporation protein HypB/0.443
2pmdGNPTranslation initiation factor 2 subunit gamma/0.443
3fql79ZGenome polyprotein2.7.7.480.443
3lfsA07Cyclin-dependent kinase 22.7.11.220.443
3pjtC2EDiguanylate cyclase/phosphodiesterase/0.443
4a28ADPKinesin-like protein KIF11/0.443
4dpmCOAMalonyl-CoA reductase1.2.1.750.443
4j7uNAPSepiapterin reductase1.1.1.1530.443
4o0uADNAurora kinase A2.7.11.10.443
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.443
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.443
5bsgNAPPyrroline-5-carboxylate reductase/0.443
5jqbIBPEnvelope glycoprotein/0.443
1b87ACOAac(6')-Ii protein/0.442
1cbrREACellular retinoic acid-binding protein 1/0.442
1g69TZPThiamine-phosphate synthase/0.442
1h6bNDPGlucose--fructose oxidoreductase1.1.99.280.442
1t9c1SMAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.442
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.442
2xpwOTCTetracycline repressor protein class D/0.442
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.442
3cisATPUniversal stress protein Rv2623/0.442
3efwAK8Aurora kinase A2.7.11.10.442
3nbzGTPGTP-binding nuclear protein Ran/0.442
4bw9ANPPyrrolysine--tRNA ligase/0.442
4c77N01Phenylacetone monooxygenase1.14.13.920.442
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.442
4i3p1CW3-hydroxyanthranilate 3,4-dioxygenase/0.442
4ie6UN9Alpha-ketoglutarate-dependent dioxygenase FTO/0.442
4in44IDKelch-like ECH-associated protein 1/0.442
4wbbADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
4xyeNADFormate dehydrogenase/0.442
5kf2ACOPredicted acetyltransferase/0.442
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.441
1nmdATPMajor actin/0.441
1pmv537Mitogen-activated protein kinase 102.7.11.240.441
1u26IHSMyo-inositol hexaphosphate phosphohydrolase/0.441
1ybmNAPUncharacterized protein At5g02240/0.441
2cahNDPCatalase1.11.1.60.441
2gs7ANPEpidermal growth factor receptor2.7.10.10.441
2qrdADP5'-AMP-activated protein kinase subunit gamma/0.441
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.441
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.441
3cgdCOACoenzyme A disulfide reductase/0.441
3daaPDDD-alanine aminotransferase2.6.1.210.441
3oibFDAPutative acyl-CoA dehydrogenase/0.441
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.441
4f4qFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.441
1efvFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.440
1fnnADPORC1-type DNA replication protein/0.440
1h6dNDPGlucose--fructose oxidoreductase1.1.99.280.440
1orkATCTetracycline repressor protein class D/0.440
2b9xFADPutative aminooxidase/0.440
2ghmLICMitogen-activated protein kinase 14/0.440
2h63NAPBiliverdin reductase A1.3.1.240.440
2imkGTXAGAP009194-PA/0.440
2xrwANPMitogen-activated protein kinase 82.7.11.240.440
3fhyATPPyridoxal kinase2.7.1.350.440
3h0sB38Acetyl-CoA carboxylase/0.440
3ictCOACoenzyme A disulfide reductase/0.440
3rf7NADIron-containing alcohol dehydrogenase/0.440
3vthAPCCarbamoyltransferase/0.440
3zlyYSODual specificity mitogen-activated protein kinase kinase 12.7.12.20.440
4an2EUIDual specificity mitogen-activated protein kinase kinase 12.7.12.20.440
4fk1FADPutative thioredoxin reductase/0.440
4u0oMTALipoyl synthase 2/0.440
4zlaBESCytosol aminopeptidase3.4.11.10.440
5a3cNADSIR2 family protein/0.440
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.440