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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
3gwwSFXNa(+):neurotransmitter symporter (Snf family)

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3gwwSFXNa(+):neurotransmitter symporter (Snf family)/1.000
2qjuDSMNa(+):neurotransmitter symporter (Snf family)/0.649
2q72IXXNa(+):neurotransmitter symporter (Snf family)/0.645
3gwuSRENa(+):neurotransmitter symporter (Snf family)/0.619
2qeiCXXNa(+):neurotransmitter symporter (Snf family)/0.564
2q6hCXXNa(+):neurotransmitter symporter (Snf family)/0.524
1y56FMNUncharacterized protein/0.500
1y56FMN382aa long hypothetical sarcosine oxidase/0.500
2ayrL4GEstrogen receptor/0.495
2yohWMJThymidylate kinase/0.493
4ivqI43Thymidine kinase/0.490
1fr8GDUBeta-1,4-galactosyltransferase 1/0.489
2qqfA1RNAD-dependent protein deacetylase HST23.5.10.487
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.10.487
3lp2LP9Gag-Pol polyprotein2.7.7.490.487
4kbn25UDihydrofolate reductase1.5.1.30.486
4yswNAIXanthine dehydrogenase/oxidase/0.481
3n0yAPCAdenylate cyclase 2/0.480
2jasDTPDeoxyguanosine kinase/0.479
2i0v6C3Macrophage colony-stimulating factor 1 receptor2.7.10.10.477
1iahADPTransient receptor potential cation channel subfamily M member 72.7.11.10.476
3njoPYVAbscisic acid receptor PYR1/0.475
4lisUPGUDP-glucose 4-epimerase (Eurofung)/0.475
2jav5Z5Serine/threonine-protein kinase Nek22.7.11.10.474
4k9yK9YFocal adhesion kinase 12.7.10.20.474
4man1Y1Apoptosis regulator Bcl-2/0.474
4m2xTMQDihydrofolate reductase1.5.1.30.473
5k2dZMAAdenosine receptor A2a/0.473
1dpmEBPParathion hydrolase3.1.8.10.471
2w3aTOPDihydrofolate reductase1.5.1.30.470
4iji99TGlutathione S-transferase-like protein YibF/0.470
4kd79DRDihydrofolate reductase1.5.1.30.470
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
3nmvPYVAbscisic acid receptor PYL2/0.469
4kvgGTPRas-related protein Rap-1A/0.469
1rfqLARActin, alpha skeletal muscle/0.468
1tkzH16Gag-Pol polyprotein2.7.7.490.468
3lbnGNPGTPase HRas/0.468
3qiyQI1Botulinum neurotoxin type A3.4.24.690.468
3fpbATPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.467
3ov4EQUSteroid Delta-isomerase5.3.3.10.467
2oyeIM8Prostaglandin G/H synthase 11.14.99.10.466
4el9AFERibosomal protein S6 kinase alpha-32.7.11.10.466
4qa0SHHHistone deacetylase 83.5.1.980.466
4x81MVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.466
5bpfADPD-alanine--D-alanine ligase/0.466
2puuG2GMitogen-activated protein kinase 14/0.465
2y4mGDXUncharacterized protein/0.465
1e2jTHMThymidine kinase/0.464
1szcCNANAD-dependent protein deacetylase HST23.5.10.464
1wbsLI2Mitogen-activated protein kinase 14/0.464
3m8cEQUSteroid Delta-isomerase5.3.3.10.464
3rs0GNPGTPase HRas/0.464
4iaq2GM5-hydroxytryptamine receptor 1B/0.464
3fkoFKOMitogen-activated protein kinase 14/0.463
3k47D09Dihydrofolate reductase1.5.1.30.463
3llaACPMyosin heavy chain kinase A2.7.11.70.463
4dyp0MSNucleoprotein/0.463
4ej1FOLDihydrofolate reductase1.5.1.30.463
4lxd1XVApoptosis regulator Bcl-2/0.463
4zs4ATPMyosin heavy chain kinase A2.7.11.70.463
1cq7PY5Aspartate aminotransferase2.6.1.10.462
1s3uTQDDihydrofolate reductase1.5.1.30.462
2zozETTranscriptional regulator/0.462
5ero210Fusicoccadiene synthase2.5.1.290.462
2amaDHTAndrogen receptor/0.461
2od7A1RNAD-dependent protein deacetylase HST23.5.10.461
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.461
3apwDP0Alpha-1-acid glycoprotein 2/0.461
3jpv1DRSerine/threonine-protein kinase pim-12.7.11.10.461
4ivrN50Thymidine kinase/0.461
4pleCPSNuclear receptor subfamily 5 group A member 2/0.461
5iu86DZAdenosine receptor A2a/0.461
1mc5AHEAlcohol dehydrogenase class-31.1.1.10.460
2vi5Y196,7-dimethyl-8-ribityllumazine synthase2.5.1.780.460
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
3itzP66Mitogen-activated protein kinase 14/0.460
2qboCAMCamphor 5-monooxygenase1.14.15.10.459
2zsdCOAPantothenate kinase2.7.1.330.459
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.459
4jbxSK7Thymidine kinase/0.459
1jjtBDSBeta-lactamase/0.458
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.458
2qimZEAClass 10 plant pathogenesis-related protein/0.458
2ydvNECAdenosine receptor A2a/0.458
3wrhCAMCamphor 5-monooxygenase1.14.15.10.458
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.458
4kfj1R0Dihydrofolate reductase1.5.1.30.458
4l4dCAMCamphor 5-monooxygenase1.14.15.10.458
4nmcFADBifunctional protein PutA/0.458
4tyj0LIFibroblast growth factor receptor 42.7.10.10.458
1w2cANPInositol-trisphosphate 3-kinase A2.7.1.1270.457
1wbtWBTMitogen-activated protein kinase 14/0.457
2a1nCAMCamphor 5-monooxygenase1.14.15.10.457
3fzsB96Protein-tyrosine kinase 2-beta2.7.10.20.457
3nefPYVAbscisic acid receptor PYL1/0.457
3uq9TBNPutative adenosine kinase/0.457
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.457
4yp05IQHistidyl-tRNA synthetase, putative/0.457
3rfmCFFAdenosine receptor A2a/0.457
2flhZEACytokinin-specific binding protein/0.456
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.456
3sa27DRDihydrofolate reductase/0.456
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.456
4dlzGNPGTPase HRas/0.456
4ds8A8SAbscisic acid receptor PYL3/0.456
1ia9ANPTransient receptor potential cation channel subfamily M member 72.7.11.10.455
1z6p194Glycogen phosphorylase, muscle form2.4.1.10.455
2p0aANPSynapsin-3/0.455
2q3eUPGUDP-glucose 6-dehydrogenase1.1.1.220.455
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.455
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.455
3ujlA8SAbscisic acid receptor PYL2/0.455
4edfUPGUDP-glucose 6-dehydrogenase1.1.1.220.455
1hfpMOTDihydrofolate reductase1.5.1.30.454
1jlcFTCGag-Pol polyprotein2.7.7.490.454
1oz1FPHMitogen-activated protein kinase 14/0.454
2y4kGDPUncharacterized protein/0.454
3juqAKDPhenazine biosynthesis protein A/B/0.454
3mvhWFERAC-alpha serine/threonine-protein kinase2.7.11.10.454
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.454
4o71CPBBromodomain-containing protein 4/0.454
4z17PEPEnolase/0.454
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.453
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.453
3h2cB58Dihydropteroate synthase/0.453
3wtiCT4Acetylcholine-binding protein/0.453
4burNADApoptosis-inducing factor 1, mitochondrial1.1.10.453
4cd2FOLDihydrofolate reductase1.5.1.30.453
4kak06UDihydrofolate reductase1.5.1.30.453
1kyzFERCaffeic acid 3-O-methyltransferase2.1.1.680.452
2rgcGNPGTPase HRas/0.452
3cfoGMPDNA-directed DNA polymerase/0.452
3dqwAGSProto-oncogene tyrosine-protein kinase Src2.7.10.20.452
3ijwACOAminoglycoside N3-acetyltransferase/0.452
3p7cP7CMitogen-activated protein kinase 14/0.452
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.452
4ek1CAMCamphor 5-monooxygenase1.14.15.10.452
4l0oPLPCystathionine gamma-synthase2.5.1.480.452
4r7uUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.452
4y6nUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.452
5ahkFADAcetolactate synthase II, large subunit/0.452
1lhvNOGSex hormone-binding globulin/0.451
1tezHDFDeoxyribodipyrimidine photo-lyase4.1.99.30.451
2f4jVX6Tyrosine-protein kinase ABL12.7.10.20.451
2vwcBC2ATP-dependent molecular chaperone HSP82/0.451
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
3mcyZH1FimH/0.451
3oafOAGDihydrofolate reductase1.5.1.30.451
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
3tdkUPGUDP-glucose 6-dehydrogenase1.1.1.220.451
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.451
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.451
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.451
1b87ACOAac(6')-Ii protein/0.450
1n5sADLActVA 6 protein/0.450
1pagFMPAntiviral protein I3.2.2.220.450
1phePIYCamphor 5-monooxygenase1.14.15.10.450
1rx4DDFDihydrofolate reductase1.5.1.30.450
1yrcCAMCamphor 5-monooxygenase1.14.15.10.450
1z6q195Glycogen phosphorylase, muscle form2.4.1.10.450
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.450
3ef5DGTProbable pyrophosphohydrolase/0.450
3gi3B10Mitogen-activated protein kinase 14/0.450
3n0z3ATAdenylate cyclase 2/0.450
3pdtADPMyosin heavy chain kinase A2.7.11.70.450
3wrlCAMCamphor 5-monooxygenase1.14.15.10.450
4bdoKAIGlutamate receptor ionotropic, kainate 2/0.450
1e3vDXCSteroid Delta-isomerase5.3.3.10.449
1hfqMOTDihydrofolate reductase1.5.1.30.449
1ove358Mitogen-activated protein kinase 14/0.449
2a4xBLMMitomycin-binding protein/0.449
2ydoADNAdenosine receptor A2a/0.449
3ar612DSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.449
3tq9MTXDihydrofolate reductase/0.449
4kaoKAOFocal adhesion kinase 12.7.10.20.449
4myq19TcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.449
4qe6JN3Bile acid receptor/0.449
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.448
1x01ATP235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase/0.448
1zzqDP9Nitric oxide synthase, brain1.14.13.390.448
2rgeGNPGTPase HRas/0.448
2yisYISMitogen-activated protein kinase 14/0.448
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.448
3gxoMQAMitomycin biosynthesis 6-O-methyltransferase/0.448
3k145352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.448
4blwSAHRibosomal RNA large subunit methyltransferase J/0.448
4dc32FAPutative adenosine kinase/0.448
4dlxGNPGTPase HRas/0.448
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4omaLCSMethionine gamma-lyase/0.448
4pd6URINucleoside permease/0.448
1f28F89Thymidylate synthase2.1.1.450.447
1ly4COQDihydrofolate reductase1.5.1.30.447
1s3wTQTDihydrofolate reductase1.5.1.30.447
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.447
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.447
3htjETEbrA repressor/0.447
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.447
3qlzQLZUncharacterized protein/0.447
3rv3ADPBiotin carboxylase6.3.4.140.447
3vhe42QVascular endothelial growth factor receptor 22.7.10.10.447
4be7ATPType I restriction enzyme EcoR124II R protein3.1.21.30.447
4eiyZMAAdenosine receptor A2a/0.447
4imu1ETNitric oxide synthase, brain1.14.13.390.447
4rkfGNPRas-related protein Rab-3/0.447
1dr4HBIDihydrofolate reductase1.5.1.30.446
1p16GTPmRNA-capping enzyme subunit alpha2.7.7.500.446
2bxe1FLSerum albumin/0.446
2e1zB4PPropionate kinase/0.446
2zscBTNTamavidin2/0.446
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.446
3mdeCO8Medium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.446
3oxk5GPHistidine triad nucleotide-binding protein30.446
4uogYYYNucleoside diphosphate kinase/0.446
1lp6C5POrotidine 5'-phosphate decarboxylase4.1.1.230.445
1yrdCAMCamphor 5-monooxygenase1.14.15.10.445
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.445
3k90A8SAbscisic acid receptor PYR1/0.445
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.445
3n1s5GPPurine nucleoside phosphoramidase/0.445
3n65XFJNitric oxide synthase, brain1.14.13.390.445
4jlt8PRCytochrome P450 2B41.14.14.10.445
4p66MTXDihydrofolate reductase/0.445
5iua6DXAdenosine receptor A2a/0.445
1gx1CDP2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.444
1ia2TQ4Dihydrofolate reductase1.5.1.30.444
1ndyFR3Adenosine deaminase3.5.4.40.444
1oh0EQUSteroid Delta-isomerase5.3.3.10.444
1pr5TBNPurine nucleoside phosphorylase DeoD-type/0.444
2bsxNOSPurine nucleoside phosphorylase/0.444
2pg2ADPKinesin-like protein KIF11/0.444
3fknFKNMitogen-activated protein kinase 14/0.444
3lbiGNPGTPase HRas/0.444
4af3VX6Aurora kinase B2.7.11.10.444
4fojC2EUncharacterized protein/0.444
4ixeIXEDihydrofolate reductase1.5.1.30.444
3qakUKAAdenosine receptor A2a/0.444
3uzaT4GAdenosine receptor A2a/0.444
1dz8CAMCamphor 5-monooxygenase1.14.15.10.443
1efvFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.443
1tl3H20Gag-Pol polyprotein2.7.7.490.443
1yhoTRRDihydrofolate reductase1.5.1.30.443
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.443
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.443
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.443
2ieiFRXGlycogen phosphorylase, muscle form2.4.1.10.443
2ph5NADHomospermidine synthase/0.443
2rjp886A disintegrin and metalloproteinase with thrombospondin motifs 43.4.24.820.443
2wwjY28Lysine-specific demethylase 4A/0.443
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.443
3af3GCPPantothenate kinase2.7.1.330.443
3c3cCDPPhosphoglycerate kinase 12.7.2.30.443
3ka7FADPutative oxidoreductase/0.443
3m4nPA9N-acetylornithine carbamoyltransferase2.1.3.90.443
3nf8CDQGag-Pol polyprotein/0.443
3p78P78Mitogen-activated protein kinase 14/0.443
3tw6ADPPyruvate carboxylase/0.443
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.443
4ho6UPGGlucose-1-phosphate thymidylyltransferase/0.443
4lvt1XJApoptosis regulator Bcl-2/0.443
5iu4ZMAAdenosine receptor A2a/0.443
4ug2NGIAdenosine receptor A2a/0.443
1dz4CAMCamphor 5-monooxygenase1.14.15.10.442
1tv8SAMGTP 3',8-cyclase4.1.99.180.442
2o2mLI0Bcl-2-like protein 1/0.442
3nnxEDDMitogen-activated protein kinase 14/0.442
4gbeSAHDNA adenine methylase2.1.1.720.442
4jlj1NMDeoxycytidine kinase2.7.1.740.442
4nyiGNPGTPase HRas/0.442
4onqSFGDNA methyltransferase/0.442
4q7hGTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
4rtmSAMDNA adenine methylase2.1.1.720.442
4zmeADNMyosin heavy chain kinase A2.7.11.70.442
1h48CDI2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.441
1sm2STUTyrosine-protein kinase ITK/TSK2.7.10.20.441
1t1sCBQ1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.441
1xpcAITEstrogen receptor/0.441
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.441
2io6330Wee1-like protein kinase2.7.10.20.441
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
3hv4L51Mitogen-activated protein kinase 14/0.441
3sglSAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.441
4dlwGNPGTPase HRas/0.441
4mubOAQSulfotransferase oxamniquine resistance protein/0.441
4qa2SHHHistone deacetylase 83.5.1.980.441
4wctFADFructosyl amine:oxygen oxidoreductase/0.441
4xoiGTPTransforming protein RhoA/0.441
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.440
1gwnGTPRho-related GTP-binding protein RhoE/0.440
1hnvTBOGag-Pol polyprotein2.7.7.490.440
1kv1BMUMitogen-activated protein kinase 14/0.440
1kv2B96Mitogen-activated protein kinase 14/0.440
1m78CLZDihydrofolate reductase1.5.1.30.440
1rs6DP2Nitric oxide synthase, brain1.14.13.390.440
1u71MXADihydrofolate reductase1.5.1.30.440
2jlbUDMUncharacterized protein/0.440
2x60GTPMannose-1-phosphate guanylyltransferase/0.440
3aca8DDADP-sugar pyrophosphatase3.6.1.130.440
3ex8AIFRiboflavin biosynthesis protein RibD1.1.1.1930.440
3jx2H4BNitric oxide synthase, brain1.14.13.390.440
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.440
3qrtX14Cyclin-dependent kinase 22.7.11.220.440
3rs4GNPGTPase HRas/0.440
4a51ADPKinesin-like protein KIF11/0.440
4dkjSAHCytosine-specific methyltransferase/0.440
4i2q1BTGag-Pol polyprotein2.7.7.490.440
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.440
4n0sDHCMitogen-activated protein kinase 12.7.11.240.440
4p68MTXDihydrofolate reductase/0.440