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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
1w2gTHMThymidylate kinase2.7.4.9

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1w2gTHMThymidylate kinase2.7.4.91.000
1n5iTMPThymidylate kinase2.7.4.90.572
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.506
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.501
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.496
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.495
2rd678PPoly [ADP-ribose] polymerase 12.4.2.300.494
1kl2FONSerine hydroxymethyltransferase/0.492
4xba5GPAprataxin-like protein30.490
1ndyFR3Adenosine deaminase3.5.4.40.488
2j7cIDEBeta-glucosidase A3.2.1.210.488
3sf6FDAGlutaryl-CoA dehydrogenase/0.488
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.486
2r7nADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase/0.484
3h3t16HCollagen type IV alpha-3-binding protein/0.483
4uugPXGBranched-chain amino acid aminotransferase, putative/0.483
1wxyFRKAdenosine deaminase3.5.4.40.480
5aqzSGVHeat shock 70 kDa protein 1A/0.480
3c36KAIGlutamate receptor ionotropic, kainate 1/0.478
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.478
1j7lADPAminoglycoside 3'-phosphotransferase2.7.1.950.476
5k2cZMAAdenosine receptor A2a/0.476
2pbzATPUncharacterized protein/0.475
2v34CTN4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.475
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.472
1hb3SCVIsopenicillin N synthase1.21.3.10.471
3fowIMHPurine nucleoside phosphorylase/0.471
3sixGDPNodulation protein Z/0.471
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.470
3biz61EWee1-like protein kinase2.7.10.20.470
3e5aVX6Aurora kinase A2.7.11.10.470
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.469
2zevIPEGeranylgeranyl pyrophosphate synthase/0.469
3sfy3FYUncharacterized protein/0.469
1z6tADPApoptotic protease-activating factor 1/0.468
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.467
3gwuSRENa(+):neurotransmitter symporter (Snf family)/0.467
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.466
4jx1CAHCamphor 5-monooxygenase1.14.15.10.466
2b8jADNClass B acid phosphatase3.1.3.20.465
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.464
1mokFAD2-oxopropyl-CoM reductase, carboxylating1.8.1.50.464
2dvlFADAcyl-CoA dehydrogenase/0.464
3p0fBAUUridine phosphorylase 22.4.2.30.463
4kxl6C62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.463
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
2zseACPPantothenate kinase2.7.1.330.462
3c35KAIGlutamate receptor ionotropic, kainate 1/0.462
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.461
1jdzFMBPurine nucleoside phosphorylase/0.461
4bb3KKAIsopenicillin N synthase1.21.3.10.461
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.460
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
3oxk5GPHistidine triad nucleotide-binding protein30.460
3v0p4GWHisto-blood group ABO system transferase/0.460
4pnmNU1Tankyrase-22.4.2.300.460
5ccyTMPPolymerase acidic protein/0.460
3a25SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.459
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4c1fX8ZMetallo-beta-lactamase type 2/0.459
5fd8A5APutative carboxypeptidase yocD/0.459
2r0cFADPutative FAD-monooxygenase/0.458
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
3mcyZH1FimH/0.458
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.458
2ieaTDPPyruvate dehydrogenase E1 component1.2.4.10.457
2w3mFOLDihydrofolate reductase1.5.1.30.457
2yohWMJThymidylate kinase/0.457
3qfrFMNNADPH--cytochrome P450 reductase/0.457
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2vcmM11Isopenicillin N synthase1.21.3.10.456
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
3q8uADPNucleoside diphosphate kinase/0.456
3qizQI2Botulinum neurotoxin type A3.4.24.690.456
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.456
2j9lATPH(+)/Cl(-) exchange transporter 5/0.455
3fnlSHALactoperoxidase/0.455
4bftZVTPantothenate kinase2.7.1.330.455
4y3jHICEndothiapepsin3.4.23.220.455
1e2nRCAThymidine kinase/0.454
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.454
1uk1FRQPoly [ADP-ribose] polymerase 12.4.2.300.454
2g263LGRenin3.4.23.150.454
3hiyUTPUncharacterized protein/0.454
4m4821BSodium-dependent dopamine transporter/0.454
4xnw2IDP2Y purinoceptor 1/0.454
1obbNADAlpha-glucosidase3.2.1.200.453
2yof74WThymidylate kinase/0.453
4lv5ADPRhoptry protein 5B/0.453
1mewXMPInosine-5'-monophosphate dehydrogenase/0.452
4y6uUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.452
1pke2FDPurine nucleoside phosphorylase DeoD-type/0.451
3vg9ZMAAdenosine receptor A2a/0.451
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.451
4mka2AYGenome polyprotein2.7.7.480.451
1k9sFM1Purine nucleoside phosphorylase DeoD-type/0.450
2wbaFADTrypanothione reductase1.8.1.120.450
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
3c34KAIGlutamate receptor ionotropic, kainate 1/0.450
3dqrJI2Nitric oxide synthase, brain1.14.13.390.450
3ebiBEYM1 family aminopeptidase3.4.110.450
3h3qH13Collagen type IV alpha-3-binding protein/0.450
3h3r14HCollagen type IV alpha-3-binding protein/0.450
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.450
4azaMGOEukaryotic translation initiation factor 4E/0.450
4gxs0YSGlutamate receptor 2/0.450
4ug71EVNitric oxide synthase oxygenase1.14.13.1650.450
1eg2MTAModification methylase RsrI2.1.1.720.449
1hk5T44Serum albumin/0.449
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.449
1rydNDPGlucose--fructose oxidoreductase1.1.99.280.449
1zg32HIIsoflavone 4'-O-methyltransferase/0.449
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.449
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.449
1g8oU5PN-acetyllactosaminide alpha-1,3-galactosyltransferase/0.448
2a3bCFFEndochitinase B13.2.1.140.448
2e93B29Geranylgeranyl pyrophosphate synthase/0.448
2zb8IMNProstaglandin reductase 21.3.1.480.448
2zdgADPD-alanine--D-alanine ligase/0.448
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
3zeiAWHO-acetylserine sulfhydrylase/0.448
4gbeSAHDNA adenine methylase2.1.1.720.448
1jnzFADAdenylylsulfate reductase, subunit A (AprA)/0.447
1kruIPTGalactoside O-acetyltransferase2.3.1.180.447
1mvtDTMDihydrofolate reductase1.5.1.30.447
1nbiSAMGlycine N-methyltransferase2.1.1.200.447
1r2jFADFkbI/0.447
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
2jb4A14Isopenicillin N synthase1.21.3.10.447
2nomDUTPoly(A) polymerase, putative/0.447
2vrjNCWBeta-glucosidase A3.2.1.210.447
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4bfxZVXPantothenate kinase2.7.1.330.447
4h6pFMNChromate reductase/0.447
4kf1HT5Aryldialkylphosphatase3.1.8.10.447
4yddMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.447
1blzACVIsopenicillin N synthase1.21.3.10.446
1rfuADPPyridoxal kinase2.7.1.350.446
2qs1UB1Glutamate receptor ionotropic, kainate 1/0.446
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.446
4gd9BTNStreptavidin/0.446
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.446
4mhtSAHModification methylase HhaI2.1.1.370.446
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.446
5k2aZMAAdenosine receptor A2a/0.446
1nbhSAMGlycine N-methyltransferase2.1.1.200.445
2hq9FADMll6688 protein/0.445
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.445
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.445
3bgxTMPThymidylate synthase/0.445
3br3ETHTH-type transcriptional regulator QacR/0.445
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4epq0RRPoly(ADP-ribose) glycohydrolase/0.445
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4rtsSAMDNA adenine methylase2.1.1.720.445
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.444
1uk0FRMPoly [ADP-ribose] polymerase 12.4.2.300.444
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.444
2vbpVB1Isopenicillin N synthase1.21.3.10.444
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3ggcH26Hypoxanthine-guanine phosphoribosyltransferase2.4.2.80.444
3tzaTZGGlutamate receptor 2/0.444
4bfvZVVPantothenate kinase2.7.1.330.444
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4fhpUTPTerminal uridylyltransferase cid1/0.444
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
5k2dZMAAdenosine receptor A2a/0.444
1pg2ADNMethionine--tRNA ligase6.1.1.100.443
2braFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.443
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2p5uNADUDP-glucose 4-epimerase/0.443
2zscBTNTamavidin2/0.443
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.443
3hu1AGSTransitional endoplasmic reticulum ATPase3.6.4.60.443
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3tdaPN0Cytochrome P450 2D6/0.443
3uk6ADPRuvB-like 23.6.4.120.443
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.442
1vbiNADMalate/L-lactate dehydrogenase family protein/0.442
1zdwFLVPrenyltransferase/0.442
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.442
4bfsZVSPantothenate kinase2.7.1.330.442
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.442
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.442
1dnpMHFDeoxyribodipyrimidine photo-lyase4.1.99.30.441
1l8aTDPPyruvate dehydrogenase E1 component1.2.4.10.441
1pd9CO4Dihydrofolate reductase1.5.1.30.441
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
1y56FMNUncharacterized protein/0.441
1y56FMN382aa long hypothetical sarcosine oxidase/0.441
1yhjR6CPyridoxal kinase2.7.1.350.441
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.441
3q7fED2Uncharacterized protein/0.441
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.441
3w5uFADFerredoxin/0.441
4gn6TYLLactoperoxidase1.11.1.70.441
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.441
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.441
1c4yIH3Prothrombin3.4.21.50.440
1jueFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.440
1kwcBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.440
1sweBTNStreptavidin/0.440
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2gqfFADUncharacterized protein HI_0933/0.440
2vi5Y196,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
3dejRXCCaspase-33.4.22.560.440
3nu03TUDihydrofolate reductase1.5.1.30.440
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.440
4bjbP34Tankyrase-22.4.2.300.440
4kc2WS2Histo-blood group ABO system transferase/0.440
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
4xp4COCSodium-dependent dopamine transporter/0.440
4zobLGCLin1840 protein/0.440
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.440