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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
1kieAD3IAG-nucleoside hydrolase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1kieAD3IAG-nucleoside hydrolase/1.000
3b9gIMHIAG-nucleoside hydrolase/0.527
3zpqXF5Beta-1 adrenergic receptor/0.490
3zj6VM2Raucaffricine-O-beta-D-glucosidase3.2.1.1250.488
1xnzFCDMethionine aminopeptidase/0.484
3k4551PDihydrofolate reductase1.5.1.30.483
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.482
2j7cIDEBeta-glucosidase A3.2.1.210.480
2x9vTMQPteridine reductase/0.480
1jdzFMBPurine nucleoside phosphorylase/0.479
2vrjNCWBeta-glucosidase A3.2.1.210.477
3h4vDVPPteridine reductase 11.5.1.330.477
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.476
2y035FWBeta-1 adrenergic receptor/0.475
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.474
3ug8IMNAldo-keto reductase family 1 member C3/0.474
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.474
2vt4P32Beta-1 adrenergic receptor/0.473
1dr4HBIDihydrofolate reductase1.5.1.30.472
1hfrMOTDihydrofolate reductase1.5.1.30.472
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.472
4dya0MFNucleoprotein/0.472
2vbvFMNRiboflavin kinase2.7.1.1610.471
4bvnP32Beta-1 adrenergic receptor/0.471
4dyp0MSNucleoprotein/0.469
4jpg1OXPyruvate kinase PKM2.7.1.400.469
3f6sFMNFlavodoxin/0.468
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.468
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.467
4k9yK9YFocal adhesion kinase 12.7.10.20.467
3c36KAIGlutamate receptor ionotropic, kainate 1/0.466
1p33MTXPteridine reductase 11.5.1.330.465
3jqgAX6Pteridine reductase, putative/0.465
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.465
3rl45GPMetallophosphoesterase MPPED23.10.465
5a4wQCTGlutathione S-transferase F22.5.1.180.465
2ycxP32Beta-1 adrenergic receptor/0.465
5d6lCAUBeta-2 adrenergic receptor/0.465
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.464
3rhjNAPCytosolic 10-formyltetrahydrofolate dehydrogenase1.5.1.60.464
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.464
1e7wMTXPteridine reductase 11.5.1.330.463
3casASD3-oxo-5-beta-steroid 4-dehydrogenase/0.463
2bf7HBIPteridine reductase 11.5.1.330.462
3bldPRFQueuine tRNA-ribosyltransferase2.4.2.290.462
4azaMGOEukaryotic translation initiation factor 4E/0.462
4xp4COCSodium-dependent dopamine transporter/0.462
4qij1HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.461
1maqPGUAspartate aminotransferase, mitochondrial2.6.1.10.460
1u1jC2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 12.1.1.140.460
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.460
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.460
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.460
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.460
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.459
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
2v57PRLTetR family transcriptional regulator/0.459
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.459
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.459
4u163C0Muscarinic acetylcholine receptor M3/0.459
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.458
1xr2C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.458
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.458
2x2rADPKinesin-like protein KIF11/0.458
3roeTHMNAD(P)H-hydrate epimerase5.1.99.60.458
1e66HUXAcetylcholinesterase3.1.1.70.457
1s7gNADNAD-dependent protein deacylase 2/0.457
2i4tUA2Purine nucleoside phosphorylase, putative/0.457
2q94A04Methionine aminopeptidase/0.457
3cr7PPSAdenylyl-sulfate kinase2.7.1.250.457
3jq6DX1Pteridine reductase, putative/0.457
3jq7DX2Pteridine reductase, putative/0.457
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.457
4l6s1WQPoly [ADP-ribose] polymerase 12.4.2.300.457
1d3dBZTProthrombin3.4.21.50.456
1e92HBIPteridine reductase 11.5.1.330.456
1pr4MTPPurine nucleoside phosphorylase DeoD-type/0.456
3htjETEbrA repressor/0.456
3rviRVIBeta-secretase 13.4.23.460.456
1mxfMTXPutative pteridine reductase 2/0.455
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.455
3occDIHPurine nucleoside phosphorylase DeoD-type/0.455
1dlrMXADihydrofolate reductase1.5.1.30.454
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.454
1q63AIQQueuine tRNA-ribosyltransferase2.4.2.290.454
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
2aouCQAHistamine N-methyltransferase2.1.1.80.454
2bfmTOPPteridine reductase 11.5.1.330.454
2io6330Wee1-like protein kinase2.7.10.20.454
3hiiPNTAmiloride-sensitive amine oxidase [copper-containing]/0.454
1e1fPSG4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.453
1hqtNAPAlcohol dehydrogenase [NADP(+)]1.1.1.20.453
2ct8MSPMethionine--tRNA ligase6.1.1.100.453
2j7dGI1Beta-glucosidase A3.2.1.210.453
2xltNA0Putative flavin-containing monooxygenase/0.453
3biz61EWee1-like protein kinase2.7.10.20.453
4amjCVDBeta-1 adrenergic receptor/0.453
4kq2U5PGlycogen [starch] synthase isoform 22.4.1.110.453
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.453
3cqeP91Wee1-like protein kinase2.7.10.20.452
3l3rOAGDihydrofolate reductase1.5.1.30.452
4gh30EVQueuine tRNA-ribosyltransferase2.4.2.290.452
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
2xugTZ4Acetylcholinesterase3.1.1.70.451
3hthPRLEbrA repressor/0.451
3jq8DX3Pteridine reductase, putative/0.451
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.451
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.451
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.451
5bn4ANPV-type ATP synthase alpha chain/0.451
1kicNOSIAG-nucleoside hydrolase/0.450
1pr6XYAPurine nucleoside phosphorylase DeoD-type/0.450
2gqnBLPCystathionine beta-lyase MetC4.4.1.80.450
2w3mFOLDihydrofolate reductase1.5.1.30.450
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.450
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.450
2q96A18Methionine aminopeptidase/0.449
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.449
4n9qFMNFMN-dependent NADH-azoreductase 1/0.449
2rh1CAUBeta-2 adrenergic receptor/0.449
1d3pBT3Prothrombin3.4.21.50.448
1x8b824Wee1-like protein kinase2.7.10.20.448
2g263LGRenin3.4.23.150.448
4eb5PLPCysteine desulfurase IscS 2/0.448
4xoqF42Coenzyme F420:L-glutamate ligase/0.448
1pke2FDPurine nucleoside phosphorylase DeoD-type/0.447
1xmmM7Gm7GpppX diphosphatase3.6.1.590.447
2uuoLK3UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.447
2xlpNAPPutative flavin-containing monooxygenase/0.447
2z2w770Wee1-like protein kinase2.7.10.20.447
3c35KAIGlutamate receptor ionotropic, kainate 1/0.447
3gyf51PDihydrofolate reductase1.5.1.30.447
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.447
5d5aCAUBeta-2 adrenergic receptor/0.447
1cq6PY4Aspartate aminotransferase2.6.1.10.446
2vq7NAPPutative flavin-containing monooxygenase/0.446
2vz0D64Pteridine reductase/0.446
2yac937Serine/threonine-protein kinase PLK12.7.11.210.446
3ptqNFGBeta-glucosidase 12/0.446
3rqwACHGamma-aminobutyric-acid receptor subunit beta-1/0.446
3w5uFADFerredoxin/0.446
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
4bjbP34Tankyrase-22.4.2.300.446
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.446
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.446
4m4821BSodium-dependent dopamine transporter/0.446
4mmf29QNa(+):neurotransmitter symporter (Snf family)/0.446
1rxjBNIStreptavidin/0.445
1z71L17Prothrombin3.4.21.50.445
2cleF6FTryptophan synthase alpha chain/0.445
2fq6P3FCystathionine beta-lyase MetC4.4.1.80.445
2pucGUNHTH-type transcriptional repressor PurR/0.445
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.445
4au7SAHHistone-lysine N-methyltransferase KMT5C2.1.1.430.445
4c2pX8ZAngiotensin-converting enzyme3.2.10.445
4dkbDUNDeoxyuridine triphosphatase, putative/0.445
2yczI32Beta-1 adrenergic receptor/0.445
4daj0HKMuscarinic acetylcholine receptor M3/0.445
2bfpH4BPteridine reductase 11.5.1.330.444
2evcFC3Methionine aminopeptidase/0.444
2q92B23Methionine aminopeptidase/0.444
2wd8VGFPteridine reductase/0.444
2yhuWHFPteridine reductase/0.444
3hf8ML0Tryptophan 5-hydroxylase 11.14.16.40.444
3jx2H4BNitric oxide synthase, brain1.14.13.390.444
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.444
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.444
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.444
4m6kFOLDihydrofolate reductase1.5.1.30.444
4u140HKMuscarinic acetylcholine receptor M3/0.444
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1uxuNAPNAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase/0.443
1zydATPeIF-2-alpha kinase GCN2/0.443
2gmsP0PPutative pyridoxamine 5-phosphate-dependent dehydrase/0.443
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.443
3lcvSAM16S rRNA (guanine(1405)-N(7))-methyltransferase2.1.1.1790.443
3n76CA23-dehydroquinate dehydratase4.2.1.100.443
4b6s2HN3-dehydroquinate dehydratase4.2.1.100.443
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.443
4fps0UXQueuine tRNA-ribosyltransferase2.4.2.290.443
4itxIN5Cystathionine beta-lyase MetC4.4.1.80.443
5dsg0HKMuscarinic acetylcholine receptor M4/0.443
1q6nP90Tyrosine-protein phosphatase non-receptor type 13.1.3.480.442
2bd0BIOSepiapterin reductase/0.442
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.442
2fzjDH3Dihydrofolate reductase1.5.1.30.442
2in6839Wee1-like protein kinase2.7.10.20.442
2vi5Y196,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.442
2z7gEH9Adenosine deaminase3.5.4.40.442
4azwSAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.442
1j7lADPAminoglycoside 3'-phosphotransferase2.7.1.950.441
1kmvLIIDihydrofolate reductase1.5.1.30.441
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
1om5H4BNitric oxide synthase, brain1.14.13.390.441
2vqbNAPPutative flavin-containing monooxygenase/0.441
2vqsBVDDeoxynucleoside kinase/0.441
3elePLPAminotransferase/0.441
3n0yAPCAdenylate cyclase 2/0.441
4a86H35Major pollen allergen Bet v 1-A/0.441
5a8eXTKBeta-1 adrenergic receptor/0.441
2qjpANJCytochrome b/0.440
2zi63D1Deoxycytidine kinase2.7.1.740.440
3gc4AAQQueuine tRNA-ribosyltransferase2.4.2.290.440
3gi2GHWDihydrofolate reductase1.5.1.30.440
4kebFOLDihydrofolate reductase1.5.1.30.440
4kfj1R0Dihydrofolate reductase1.5.1.30.440
4rtbSAMPutative thiazole biosynthesis protein ThiH/0.440