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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
5k0t415Methionine--tRNA ligase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
5k0t415Methionine--tRNA ligase/1.000
5k0s0OUMethionine--tRNA ligase/0.744
4py243EMethionine--tRNA ligase/0.601
3arvSAUChitinase A/0.491
3drcMTXDihydrofolate reductase1.5.1.30.488
1s3uTQDDihydrofolate reductase1.5.1.30.485
1y9r1CAMineralocorticoid receptor/0.483
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.483
1oc1ASVIsopenicillin N synthase1.21.3.10.480
3mnpDEXGlucocorticoid receptor/0.480
2ibzUQ6Cytochrome b/0.479
1w06W05Isopenicillin N synthase1.21.3.10.476
1qk35GPHypoxanthine-guanine-xanthine phosphoribosyltransferase2.4.2.220.475
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.475
2duv371Cyclin-dependent kinase 22.7.11.220.474
2vttLZDCyclin-dependent kinase 22.7.11.220.474
3fwgCAMCamphor 5-monooxygenase1.14.15.10.474
2po7CHDFerrochelatase, mitochondrial4.99.1.10.472
4lsjLSJGlucocorticoid receptor/0.472
1m17AQ4Epidermal growth factor receptor2.7.10.10.471
2abi1CAMineralocorticoid receptor/0.471
2jb4A14Isopenicillin N synthase1.21.3.10.471
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.470
1ke5LS1Cyclin-dependent kinase 22.7.11.220.470
1fm4DXCMajor pollen allergen Bet v 1-L/0.469
1t85CAMCamphor 5-monooxygenase1.14.15.10.469
2j9gANPBiotin carboxylase6.3.4.140.469
2vcmM11Isopenicillin N synthase1.21.3.10.469
4ejh0QACytochrome P450 2A131.14.14.10.469
1tj0FADBifunctional protein PutA1.5.5.20.468
3rpy27ZCyclin-dependent kinase 22.7.11.220.468
4nmbFADBifunctional protein PutA/0.468
3kjgADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.467
1r2jFADFkbI/0.466
1svlADPLarge T antigen3.6.40.466
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.466
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.466
4a84DXCMajor pollen allergen Bet v 1-A/0.466
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.466
5irnADPNucleotide binding oligomerization domain containing 2/0.466
1hb3SCVIsopenicillin N synthase1.21.3.10.465
2w06FRVCyclin-dependent kinase 22.7.11.220.465
2w17I19Cyclin-dependent kinase 22.7.11.220.465
2xlsFADPutative flavin-containing monooxygenase/0.465
3oxfSAHHistone-lysine N-methyltransferase SMYD32.1.1.430.465
2aa71CAMineralocorticoid receptor/0.464
2iw84SPCyclin-dependent kinase 22.7.11.220.464
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.464
2w0bCMWLanosterol 14-alpha demethylase1.14.13.700.464
1lcbDHFThymidylate synthase/0.463
1mvtDTMDihydrofolate reductase1.5.1.30.463
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.462
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.462
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.462
3nefPYVAbscisic acid receptor PYL1/0.462
4h3f10OBeta-secretase 13.4.23.460.462
4oplFDAConserved Archaeal protein/0.462
1obnASVIsopenicillin N synthase1.21.3.10.461
2c4iBTNAvidin/0.461
2iviACWIsopenicillin N synthase1.21.3.10.461
2izlIMIStreptavidin/0.461
2rtdBTNStreptavidin/0.461
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.461
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.460
3lfeZ84Mitogen-activated protein kinase 14/0.460
3zoiM2WIsopenicillin N synthase1.21.3.10.460
4bmoFMNProtein NrdI/0.460
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
5dstSAHProtein arginine N-methyltransferase 82.1.10.460
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
2bxmIMNSerum albumin/0.459
3g5kBB2Peptide deformylase, mitochondrial3.5.1.880.459
5bp9SAHPutative methyltransferase protein/0.459
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.459
1pd9CO4Dihydrofolate reductase1.5.1.30.458
1pdhFASp-hydroxybenzoate hydroxylase/0.458
2wdqCBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.458
2wdqCBESuccinate dehydrogenase cytochrome b556 subunit/0.458
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.458
4xz3COAAcyl-CoA synthetase (NDP forming)/0.458
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
1n83CLRNuclear receptor ROR-alpha/0.457
1oiyN41Cyclin-dependent kinase 22.7.11.220.457
2zbaZBATrichothecene 3-O-acetyltransferase/0.457
3py0SU9Cyclin-dependent kinase 22.7.11.220.457
3sp9IL2Peroxisome proliferator-activated receptor delta/0.457
3wrmCAMCamphor 5-monooxygenase1.14.15.10.457
4frkDWDBeta-secretase 13.4.23.460.457
4y9lFADAcyl-CoA dehydrogenase family member 11/0.457
1jg0DDTThymidylate synthase/0.456
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.456
6cp4CAMCamphor 5-monooxygenase1.14.15.10.456
1y52BTNAvidin-related protein 4/5/0.455
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3up0D7SaceDAF-12/0.455
4bmpFMNProtein NrdI/0.455
2c7gFADNADPH-ferredoxin reductase FprA1.18.1.20.454
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
2vbpVB1Isopenicillin N synthase1.21.3.10.454
2y60M8FIsopenicillin N synthase1.21.3.10.454
3c35KAIGlutamate receptor ionotropic, kainate 1/0.454
3imeBZ2Pantothenate synthetase6.3.2.10.454
3qzgX67Cyclin-dependent kinase 22.7.11.220.454
4n57ADPAPH(2'')-Id/0.454
4okt198Androgen receptor/0.454
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.454
1fvv107Cyclin-dependent kinase 22.7.11.220.453
1hb1OCVIsopenicillin N synthase1.21.3.10.453
1jtuLYBThymidylate synthase/0.453
2aaxPDNMineralocorticoid receptor/0.453
2uz2BTNAvd protein/0.453
4a81DXCMajor pollen allergen Bet v 1-A/0.453
4dymIYZActivin receptor type-12.7.11.300.453
4o8aFADBifunctional protein PutA1.2.1.880.453
1dajMOTDihydrofolate reductase1.5.1.30.452
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
2qbnCAMCamphor 5-monooxygenase1.14.15.10.452
3fwjCAMCamphor 5-monooxygenase1.14.15.10.452
3vmmP0DAlanine--anticapsin ligase/0.452
4z34ON7Lysophosphatidic acid receptor 1/0.452
1aq1STUCyclin-dependent kinase 22.7.11.220.451
1hfqMOTDihydrofolate reductase1.5.1.30.451
1jkx138Phosphoribosylglycinamide formyltransferase/0.451
1njaDCMThymidylate synthase/0.451
1swtBTNStreptavidin/0.451
1urwI1PCyclin-dependent kinase 22.7.11.220.451
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.451
2vv9IM9Cyclin-dependent kinase 22.7.11.220.451
2y9qANPMitogen-activated protein kinase 12.7.11.240.451
3akkADPSerine/threonine-protein kinase CtkA2.7.11.10.451
3dpd41APhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
3qj5022Alcohol dehydrogenase class-31.1.1.10.451
3rk708ZCyclin-dependent kinase 22.7.11.220.451
4aosNAPSteroid monooxygenase/0.451
4ezl0SEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4i13FOLDihydrofolate reductase1.5.1.30.451
4mv8ACPBiotin carboxylase6.3.4.140.451
1f4fTP3Thymidylate synthase/0.450
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.450
2izfBTNStreptavidin/0.450
3mtfA3FActivin receptor type-12.7.11.300.450
4okb198Androgen receptor/0.450
4udaDEXMineralocorticoid receptor/0.450
1j1zATPArgininosuccinate synthase/0.449
1t87CAMCamphor 5-monooxygenase1.14.15.10.449
2rehFADNitroalkane oxidase1.7.3.10.449
2vn0TDZCytochrome P450 2C8/0.449
3ezvEZVCyclin-dependent kinase 22.7.11.220.449
3gphOIDCytochrome P450 2E11.14.130.449
3junAKDPhenazine biosynthesis protein A/B/0.449
3rdqDTBStreptavidin/0.449
3zr7OR8Progesterone receptor/0.449
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.449
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.449
1mvsDTMDihydrofolate reductase1.5.1.30.448
1o6qR17Squalene--hopene cyclase4.2.1.1290.448
2bu9HFVIsopenicillin N synthase1.21.3.10.448
2gblATPCircadian clock protein kinase KaiC2.7.11.10.448
2rqfJH3Hemolymph juvenile hormone binding protein/0.448
2wo7ASVIsopenicillin N synthase1.21.3.10.448
3ibqATPPyridoxal kinase/0.448
4fkpLS5Cyclin-dependent kinase 22.7.11.220.448
4g67SAHUncharacterized ACR, COG1565 superfamily/0.448
4g8bHL6Alpha/beta hydrolase fold protein/0.448
4nm9FADBifunctional protein PutA/0.448
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.447
1kzjCB3Thymidylate synthase/0.447
1ot7IU5Bile acid receptor/0.447
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.447
2ociTYCValacyclovir hydrolase3.10.447
2qbmCAMCamphor 5-monooxygenase1.14.15.10.447
2y6fM9FIsopenicillin N synthase1.21.3.10.447
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.447
3qeoLLTDeoxycytidine kinase2.7.1.740.447
3vt3VDXVitamin D3 receptor/0.447
4hxn1A7Bromodomain-containing protein 4/0.447
4lr61XABromodomain-containing protein 4/0.447
4p6xHCYGlucocorticoid receptor/0.447
1jmgUMPThymidylate synthase/0.446
1pxpCK8Cyclin-dependent kinase 22.7.11.220.446
1t86CAMCamphor 5-monooxygenase1.14.15.10.446
1tj1FADBifunctional protein PutA1.5.5.20.446
1vruAAPGag-Pol polyprotein2.7.7.490.446
2acwUPGGlycosyltransferase/0.446
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.446
2pmoHMDProtein kinase 7/0.446
2rteBTNStreptavidin/0.446
2uxuNARHTH-type transcriptional regulator TtgR/0.446
3lanKBTGag-Pol polyprotein2.7.7.490.446
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4jr7GNPCasein kinase II subunit alpha2.7.11.10.446
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.446
1i9hBNIStreptavidin/0.445
1o76CAMCamphor 5-monooxygenase1.14.15.10.445
1oitHDTCyclin-dependent kinase 22.7.11.220.445
1phePIYCamphor 5-monooxygenase1.14.15.10.445
1upw444Oxysterols receptor LXR-beta/0.445
2fhnBNIAvidin-related protein 4/5/0.445
2qo9ANPEphrin type-A receptor 32.7.10.10.445
2uxpCLMHTH-type transcriptional regulator TtgR/0.445
2xj2985Serine/threonine-protein kinase pim-12.7.11.10.445
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3r1sX73Cyclin-dependent kinase 22.7.11.220.445
3rm8RM8Acidic mammalian chitinase3.2.1.140.445
3t3r9PLCytochrome P450 2A61.14.130.445
4jhz1KVBeta-glucuronidase3.2.1.310.445
4kos4KOUncharacterized protein/0.445
1coyANDCholesterol oxidase1.1.3.60.444
1df7MTXDihydrofolate reductase1.5.1.30.444
1qiqACCIsopenicillin N synthase1.21.3.10.444
1tv8SAMGTP 3',8-cyclase4.1.99.180.444
2jn3JN3Fatty acid-binding protein, liver/0.444
2ojg19AMitogen-activated protein kinase 12.7.11.240.444
2xvv9DNSerum albumin/0.444
3cppCAMCamphor 5-monooxygenase1.14.15.10.444
3h3t16HCollagen type IV alpha-3-binding protein/0.444
3hazFADBifunctional protein PutA/0.444
3ictFADCoenzyme A disulfide reductase/0.444
3n0tOPYDipeptidyl peptidase 23.4.14.20.444
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.444
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4deg0JJHepatocyte growth factor receptor2.7.10.10.444
4eilUMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
4fkv61KCyclin-dependent kinase 22.7.11.220.444
4l4bCAMCamphor 5-monooxygenase1.14.15.10.444
4qjqOTRLactoperoxidase/0.444
4rvnCOAPhenylacetate-coenzyme A ligase/0.444
4uohADPNucleoside diphosphate kinase/0.444
5akk1P8Bifunctional epoxide hydrolase 23.1.3.760.444
1vzaUMPThymidylate synthase/0.443
2ibtNEAModification methylase TaqI2.1.1.720.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
2w6pOA4Biotin carboxylase6.3.4.140.443
2w6qOA5Biotin carboxylase6.3.4.140.443
3c3aADPPhosphoglycerate kinase 12.7.2.30.443
3ry2BTNStreptavidin/0.443
3s1dZIRCytokinin dehydrogenase 11.5.99.120.443
3zraORBProgesterone receptor/0.443
4g1z0VPVitamin D3 receptor A/0.443
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.443
4oeaDHTAndrogen receptor/0.443
1bk0ACVIsopenicillin N synthase1.21.3.10.442
1cqp803Integrin alpha-L/0.442
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.442
2c3qGTXGlutathione S-transferase theta-12.5.1.180.442
2cchATPCyclin-dependent kinase 22.7.11.220.442
2i1vADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.442
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.442
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.442
2xw19NVSerum albumin/0.442
3gwuSRENa(+):neurotransmitter symporter (Snf family)/0.442
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
3qarQARPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.442
4dpy2P0Mevalonate diphosphate decarboxylase/0.442
4edy9PQHematopoietic prostaglandin D synthase/0.442
4ful0VUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4imfSI3N-acetylneuraminate lyase/0.442
4j0r1H2Bromodomain-containing protein 4/0.442
4j6cSTRCytochrome P450 monooxygenase/0.442
4l64C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.442
1m8h6NINitric oxide synthase, inducible1.14.13.390.441
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1sriDMBStreptavidin/0.441
1uyuCAMCamphor 5-monooxygenase1.14.15.10.441
1zdwFLVPrenyltransferase/0.441
2bfrADP[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.441
2g97DGBNicotinamide phosphoribosyltransferase2.4.2.120.441
2j62GSZO-GlcNAcase NagJ/0.441
2oaxSNLMineralocorticoid receptor/0.441
2ykeYKEHeat shock protein HSP 90-alpha/0.441
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.441
3mnoDEXGlucocorticoid receptor/0.441
3nguADPNucleoside diphosphate kinase/0.441
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.441
3pe2E1BCasein kinase II subunit alpha2.7.11.10.441
3wrjCAMCamphor 5-monooxygenase1.14.15.10.441
4a83DXCMajor pollen allergen Bet v 1-A/0.441
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4dc0NDPPutative ketoacyl reductase1.3.10.441
4g3rCAMCamphor 5-monooxygenase1.14.15.10.441
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.441
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1bc5SAHChemotaxis protein methyltransferase2.1.1.800.440
1dz4CAMCamphor 5-monooxygenase1.14.15.10.440
1osvCHCBile acid receptor/0.440
1p0hACOMycothiol acetyltransferase2.3.1.1890.440
1qjfACSIsopenicillin N synthase1.21.3.10.440
1s3yTQTDihydrofolate reductase1.5.1.30.440
1uzwCDHIsopenicillin N synthase1.21.3.10.440
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2ab8MTPAdenosine kinase2.7.1.200.440
2cy2ACOProbable acetyltransferase/0.440
2fszOHTEstrogen receptor beta/0.440
2w9hTOPDihydrofolate reductase1.5.1.30.440
3g6zA7TRenin3.4.23.150.440
3gwfNAPCyclohexanone monooxygenase/0.440
3h3r14HCollagen type IV alpha-3-binding protein/0.440
3oogYTPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
3t7qRB4Endothiapepsin3.4.23.220.440
3zc5W9ZHepatocyte growth factor receptor2.7.10.10.440
4p6wMOFGlucocorticoid receptor/0.440
5iua6DXAdenosine receptor A2a/0.440
3qakUKAAdenosine receptor A2a/0.440