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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
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/1.000
1rm4NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.614
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.607
3dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.601
3zcxNADGlyceraldehyde-3-phosphate dehydrogenase/0.596
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/0.594
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.594
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.593
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.589
2dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.588
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.588
3k2bNADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.582
1vc2NADGlyceraldehyde-3-phosphate dehydrogenase/0.580
1gd1NADGlyceraldehyde-3-phosphate dehydrogenase/0.575
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.574
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.573
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.570
2d2iNAPGlyceraldehyde-3-phosphate dehydrogenase/0.569
3lvfNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.569
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.568
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.566
2pkrNDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.563
1nboNADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.557
1jn0NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.553
1a7kNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.551
1rm3NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.551
1gypNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.550
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.550
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.548
3l4sNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.545
1ml3NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.535
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.534
3gnqNADGlyceraldehyde-3-phosphate dehydrogenase/0.531
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.530
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.523
2b4rNADGlyceraldehyde-3-phosphate dehydrogenase/0.517
1vsvNADGlyceraldehyde-3-phosphate dehydrogenase/0.512
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase/0.510
3pymNADGlyceraldehyde-3-phosphate dehydrogenase 31.2.1.120.510
1ihxSNDGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.504
1gadNADGlyceraldehyde-3-phosphate dehydrogenase A/0.503
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.503
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.503
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.502
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.496
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.490
1cerNADGlyceraldehyde-3-phosphate dehydrogenase/0.489
2ft9CHDFatty acid-binding protein 2, liver/0.475
3ad9NADSubunit alpha of sarocosine oxidase/0.474
3l0dNADGlyceraldehyde-3-phosphate dehydrogenase/0.473
4cukNAID-lactate dehydrogenase/0.471
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.469
1pdhFASp-hydroxybenzoate hydroxylase/0.466
4ipw1G7Mycocyclosin synthase1.14.21.90.465
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.465
4q73FADBifunctional protein PutA/0.464
4yqfGDPSeptin-9/0.463
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.462
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.460
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.459
3rasNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.457
3u9eCOALmo1369 protein/0.457
4a4zANPAntiviral helicase SKI23.6.4.130.457
4bb3KKAIsopenicillin N synthase1.21.3.10.457
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
4f07FADStyrene monooxygenase component 2/0.455
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
3d5m4MSGenome polyprotein2.7.7.480.454
4qxr1YEStimulator of interferon genes protein/0.454
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.453
2y4gTIRTamL/0.453
3to3ATPPetrobactin biosynthesis protein AsbB/0.453
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
5kghACOPredicted acetyltransferase/0.453
1gcoNADGlucose 1-dehydrogenase1.1.1.470.451
3zc3NAPFerredoxin--NADP reductase1.18.1.20.451
4i6gFADCryptochrome-2/0.451
1ykdCMPAdenylate cyclase/0.450
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.450
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.450
3uylTYDProbable NDP-rhamnosyltransferase/0.449
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
1dssNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.448
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.448
4o671SYCyclic GMP-AMP synthase/0.448
1jioDEB6-deoxyerythronolide B hydroxylase/0.447
3adaNADSubunit alpha of sarocosine oxidase/0.447
3golXNDGenome polyprotein2.7.7.480.446
4ejmNAPPutative zinc-binding dehydrogenase/0.446
5d3qGDPDynamin-13.6.5.50.446
3kb1ADPIron-sulfur cluster carrier protein/0.445
3nmpPYVAbscisic acid receptor PYL2/0.445
4m4922YL-lactate dehydrogenase A chain1.1.1.270.445
1xe55FEPlasmepsin-23.4.23.390.444
2r7pANPNon-structural protein 23.6.40.444
2y3sTIRTamL/0.444
3ziaATPATP synthase subunit alpha, mitochondrial/0.444
5bsfNADPyrroline-5-carboxylate reductase/0.444
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.443
2rhrEMOPutative ketoacyl reductase1.3.10.443
1g6kNADGlucose 1-dehydrogenase1.1.1.470.442
3oetNADErythronate-4-phosphate dehydrogenase/0.442
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.442
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.442
4yswFADXanthine dehydrogenase/oxidase/0.442
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.441
2fznFADBifunctional protein PutA1.5.5.20.441
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.441
3lqfNADGalactitol dehydrogenase/0.441
4b1rITCTetracycline repressor protein class D/0.441
4ips1G4Mycocyclosin synthase1.14.21.90.441
4is3NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 21.17.98.10.441
4k6fNAPPutative Acetoacetyl-CoA reductase/0.441
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.440
2itqITQEpidermal growth factor receptor2.7.10.10.440
2qo7ANPEphrin type-A receptor 32.7.10.10.440
2y3rTRKTamL/0.440
4bqh9VUUDP-N-acetylglucosamine pyrophosphorylase, putative/0.440
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.440