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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
4bdrKAIGlutamate receptor ionotropic, kainate 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4bdrKAIGlutamate receptor ionotropic, kainate 2/1.000
2xxvKAIGlutamate receptor ionotropic, kainate 2/0.675
3c36KAIGlutamate receptor ionotropic, kainate 1/0.628
4bdoKAIGlutamate receptor ionotropic, kainate 2/0.617
3c34KAIGlutamate receptor ionotropic, kainate 1/0.610
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.608
3c35KAIGlutamate receptor ionotropic, kainate 1/0.590
3kfmKAIGlutamate receptor 4/0.581
4f3gKAIGlutamate receptor 3/0.580
2xxyKAIGlutamate receptor ionotropic, kainate 2/0.556
1lbbKAIGlutamate receptor 2/0.554
1fw0KAIGlutamate receptor 2/0.553
4h8i11WGlutamate receptor ionotropic, kainate 2/0.553
4f31KAIGlutamate receptor 3/0.527
3lfzADPUncharacterized protein MJ1225/0.522
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.517
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.500
1ftlDNQGlutamate receptor 2/0.497
1mewXMPInosine-5'-monophosphate dehydrogenase/0.493
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.491
2bakAQZMitogen-activated protein kinase 14/0.491
3mflDHYProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.491
3mflDHYProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.491
4a9yAQZMitogen-activated protein kinase 14/0.491
1w7h3IPMitogen-activated protein kinase 14/0.490
3be2RAJVascular endothelial growth factor receptor 22.7.10.10.490
3to3ATPPetrobactin biosynthesis protein AsbB/0.486
3gcq1BUMitogen-activated protein kinase 14/0.485
4dldTZGGlutamate receptor ionotropic, kainate 1/0.481
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.480
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.480
1pxgPRFQueuine tRNA-ribosyltransferase2.4.2.290.479
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.479
3biz61EWee1-like protein kinase2.7.10.20.479
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.479
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.477
4k37SAMAnaerobic sulfatase-maturating enzyme1.8.980.477
2nnqT4BFatty acid-binding protein, adipocyte/0.476
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.475
1touB1VFatty acid-binding protein, adipocyte/0.473
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.473
4bis8HQLysine-specific demethylase 4A1.14.110.473
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.472
4imfSI3N-acetylneuraminate lyase/0.472
2fjeFADAdenylylsulfate reductase, subunit A (AprA)/0.471
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.471
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.471
3c3eFO12-phospho-L-lactate transferase/0.470
3mauEXTPutative sphingosine-1-phosphate lyase/0.470
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.470
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.469
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.468
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.468
1w1wAGSStructural maintenance of chromosomes protein 1/0.467
3bi6396Wee1-like protein kinase2.7.10.20.467
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.467
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.466
1towCRZFatty acid-binding protein, adipocyte/0.465
1w6rGNTAcetylcholinesterase3.1.1.70.465
3cr0809Wee1-like protein kinase2.7.10.20.465
4pkwGM6Lethal factor3.4.24.830.465
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
3fpbATPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.463
1zgaHMKIsoflavone 4'-O-methyltransferase/0.462
3hr4FMNNitric oxide synthase, inducible1.14.13.390.462
4gxs0YSGlutamate receptor 2/0.462
1p33MTXPteridine reductase 11.5.1.330.461
2b8jADNClass B acid phosphatase3.1.3.20.461
1fmjRTLRetinol dehydratase/0.460
2b82ADNClass B acid phosphatase3.1.3.20.460
2xjc5GPCytosolic purine 5'-nucleotidase3.1.3.50.460
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3phcIM5Purine nucleoside phosphorylase/0.460
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.459
2cekN8TAcetylcholinesterase3.1.1.70.459
3hv3R49Mitogen-activated protein kinase 14/0.459
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.459
3uk6ADPRuvB-like 23.6.4.120.459
4c6zTLE3-oxoacyl-ACP synthase/0.459
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.458
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.457
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
2fjaFADAdenylylsulfate reductase, subunit A (AprA)/0.457
3q9bB3NAcetylpolyamine amidohydrolase/0.457
4lb9EVPSerum albumin/0.457
1giqNAIIota toxin component Ia/0.456
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.456
2owb626Serine/threonine-protein kinase PLK12.7.11.210.456
2v58LZJBiotin carboxylase6.3.4.140.456
5dozNDPJamJ/0.456
1nw4IMHPurine nucleoside phosphorylase/0.455
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.455
4b6uM7GEukaryotic translation initiation factor 4E type 3/0.455
2gfsPQBMitogen-activated protein kinase 14/0.454
2in6839Wee1-like protein kinase2.7.10.20.454
2wkyIBCGlutamate receptor ionotropic, kainate 1/0.454
3fr5I4AFatty acid-binding protein, adipocyte/0.454
4gh10WXQueuine tRNA-ribosyltransferase2.4.2.290.454
4qjcIXEDihydrofolate reductase1.5.1.30.454
1h83FADPolyamine oxidase1.5.3.140.452
2g8yNADHydroxycarboxylate dehydrogenase B/0.452
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.452
3cb2GDPTubulin gamma-1 chain/0.452
1votHUPAcetylcholinesterase3.1.1.70.451
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.451
2zs9ADPPantothenate kinase2.7.1.330.451
3n87N873-dehydroquinate dehydratase4.2.1.100.451
3q44D50M1 family aminopeptidase3.4.110.451
4uy6SAHHistidine N-alpha-methyltransferase/0.451
1n3sGTPGTP cyclohydrolase 13.5.4.160.450
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.450
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.450
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.450
3hk1B64Fatty acid-binding protein, adipocyte/0.450
3ufl508Beta-secretase 13.4.23.460.450
3v2uATPProtein GAL3/0.450
3vf60H6Glucokinase2.7.1.20.450
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.450
4y1bNAPAntE/0.450
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.449
1gpnHUBAcetylcholinesterase3.1.1.70.449
1pf7IMHPurine nucleoside phosphorylase2.4.2.10.449
2xi4AFTAcetylcholinesterase3.1.1.70.449
2yac937Serine/threonine-protein kinase PLK12.7.11.210.449
3bi2FADPolyamine oxidase FMS1/0.449
3dhbC6LN-acyl homoserine lactonase AiiA3.1.1.810.449
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.449
3ihgVAKAklavinone 12-hydroxylase RdmE/0.449
3rvhHQ2Lysine-specific demethylase 4A1.14.110.449
3sl2ATPSensor histidine kinase WalK/0.449
3uayADNPurine nucleoside phosphorylase DeoD-type/0.449
3ungADPCRISPR system Cmr subunit Cmr2/0.449
3v0p4GWHisto-blood group ABO system transferase/0.449
4b65NDPL-ornithine N(5)-monooxygenase/0.449
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.449
4twnB96Ephrin type-A receptor 32.7.10.10.449
1nbiSAMGlycine N-methyltransferase2.1.1.200.448
1p0pBCHCholinesterase3.1.1.80.448
1pqc444Oxysterols receptor LXR-beta/0.448
1yqj6NPMitogen-activated protein kinase 14/0.448
2a9z26AAdenosine kinase2.7.1.200.448
2aqbTL63-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.448
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.448
2v59LZKBiotin carboxylase6.3.4.140.448
3wqtANPCell division protein FtsA/0.448
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.448
4ho6UTPGlucose-1-phosphate thymidylyltransferase/0.448
1bk0ACVIsopenicillin N synthase1.21.3.10.447
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
3ojxFMNNADPH--cytochrome P450 reductase/0.447
4h0yNADIota toxin component Ia/0.447
2on6IMHPurine nucleoside phosphorylase2.4.2.10.446
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.446
2wu4HBPAcetylcholinesterase3.1.1.70.446
3dz7O8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.446
3iktNADRedox-sensing transcriptional repressor Rex/0.446
3lfeZ84Mitogen-activated protein kinase 14/0.446
3v0m5GWHisto-blood group ABO system transferase/0.446
3zkyWT4Isopenicillin N synthase1.21.3.10.446
4dk70KSOxysterols receptor LXR-beta/0.446
4fhd0TTSpore photoproduct lyase/0.446
4mv4ACPBiotin carboxylase6.3.4.140.446
1e7wMTXPteridine reductase 11.5.1.330.445
2x96RX3Angiotensin-converting enzyme3.4.15.10.445
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4gdpFADPolyamine oxidase FMS1/0.445
4jbtASDCytochrome P450 monooxygenase/0.445
4mqt2CUMuscarinic acetylcholine receptor M2/0.445
1pr5TBNPurine nucleoside phosphorylase DeoD-type/0.444
1vbiNADMalate/L-lactate dehydrogenase family protein/0.444
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.444
2qxxTTPdCTP deaminase3.5.4.130.444
3aklADPSerine/threonine-protein kinase CtkA2.7.11.10.444
3bldPRFQueuine tRNA-ribosyltransferase2.4.2.290.444
4b7zQ4QAcetylcholinesterase3.1.1.70.444
4c717RD3-oxoacyl-ACP synthase/0.444
4ey6GNTAcetylcholinesterase3.1.1.70.444
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.444
4j6dTESCytochrome P450 monooxygenase/0.444
4lrrCF9Thymidylate synthase/0.444
4zzjCNANAD-dependent protein deacetylase sirtuin-13.5.10.444
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.443
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3fowIMHPurine nucleoside phosphorylase/0.443
3itzP66Mitogen-activated protein kinase 14/0.443
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.443
4f1yCNIGlutamate receptor 3/0.443
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.442
1crbRTLRetinol-binding protein 1/0.442
1dr3HBIDihydrofolate reductase1.5.1.30.442
1kmvLIIDihydrofolate reductase1.5.1.30.442
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2xtkAZMClass III chitinase ChiA1/0.442
2xvu9DNSerum albumin/0.442
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.442
3h0wN8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.442
3iaaTYDCalG2/0.442
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.442
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.442
3pchCHBProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.442
4b6r3DQ3-dehydroquinate dehydratase4.2.1.100.442
4m4821BSodium-dependent dopamine transporter/0.442
4req5ADMethylmalonyl-CoA mutase large subunit5.4.99.20.442
4s1iPLPPyridoxal kinase, putative/0.442
5dp2NAPCurF/0.442
1kl2FONSerine hydroxymethyltransferase/0.441
2x90EALAngiotensin-converting enzyme3.4.15.10.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3pe2E1BCasein kinase II subunit alpha2.7.11.10.441
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.441
4ts9FMCPurine nucleoside phosphorylase DeoD-type/0.441
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1ozqPRFQueuine tRNA-ribosyltransferase2.4.2.290.440
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.440
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.440
1rzuADPGlycogen synthase 12.4.1.210.440
2db3ANPATP-dependent RNA helicase vasa, isoform A3.6.4.130.440
2emuSAHDiphthine synthase/0.440
2r0cFADPutative FAD-monooxygenase/0.440
2xytTC9Soluble acetylcholine receptor/0.440
3i2834NBifunctional epoxide hydrolase 23.3.2.100.440
3qbwADPAnhydro-N-acetylmuramic acid kinase/0.440
3rtnRTNBeta-secretase 13.4.23.460.440
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
4a16H34Acetylcholinesterase3.1.1.70.440