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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
4i1iNADMalate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4i1iNADMalate dehydrogenase/1.000
3gvhNADMalate dehydrogenase/0.567
2aa3AP0L-lactate dehydrogenase/0.553
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.548
3d4pNADL-lactate dehydrogenase 11.1.1.270.546
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.535
4rlsNAIL-lactate dehydrogenase A chain1.1.1.270.530
2x0iNAIMalate dehydrogenase/0.524
1ez4NADL-lactate dehydrogenase1.1.1.270.521
1guyNADMalate dehydrogenase/0.517
1b8uNADMalate dehydrogenase/0.509
1uxjNADMalate dehydrogenase/0.507
1ur5NADMalate dehydrogenase/0.506
3wswNADL-lactate dehydrogenase/0.502
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.501
4gl4NAIAlcohol dehydrogenase class-3/0.496
1t2cNAIL-lactate dehydrogenase1.1.1.270.488
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.486
1bdmNAXMalate dehydrogenase/0.484
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.484
3lqfNADGalactitol dehydrogenase/0.482
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.482
1wziNDPMalate dehydrogenase/0.481
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.481
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.481
4uunNAIL-lactate dehydrogenase/0.481
5a1tNAIL-lactate dehydrogenase/0.481
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.480
4k6fNAPPutative Acetoacetyl-CoA reductase/0.480
1xe55FEPlasmepsin-23.4.23.390.479
1obbNADAlpha-glucosidase3.2.1.200.478
2ldbNADL-lactate dehydrogenase1.1.1.270.476
3imgBZ2Pantothenate synthetase6.3.2.10.476
1gv0NADMalate dehydrogenase/0.475
3qt62P0Mevalonate diphosphate decarboxylase/0.475
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.474
1wzeNADMalate dehydrogenase/0.473
1xe65FPPlasmepsin-23.4.23.390.472
4i9h1E4L-lactate dehydrogenase A chain1.1.1.270.469
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.467
1uxkNADMalate dehydrogenase/0.466
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.466
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.465
1b8vNADMalate dehydrogenase/0.463
3c212BADNA integrity scanning protein DisA/0.463
1qrpHH0Pepsin A-43.4.23.10.460
4dptAGSMevalonate diphosphate decarboxylase/0.460
1bmdNADMalate dehydrogenase/0.459
2dftADPShikimate kinase2.7.1.710.459
3kb1ADPIron-sulfur cluster carrier protein/0.459
4yxm2BADNA integrity scanning protein DisA/0.459
1tehNADAlcohol dehydrogenase class-31.1.1.10.457
2c20NADUDP-glucose 4-epimerase/0.457
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.457
3uylTYDProbable NDP-rhamnosyltransferase/0.457
1ma0NADAlcohol dehydrogenase class-31.1.1.10.456
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.456
4a83DXCMajor pollen allergen Bet v 1-A/0.455
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.455
1emdNADMalate dehydrogenase/0.454
3isjA8DPantothenate synthetase6.3.2.10.454
3mk6ACOPantothenate kinase 32.7.1.330.454
2a94AP0L-lactate dehydrogenase1.1.1.270.453
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.453
1f8fNADBenzyl alcohol dehydrogenase/0.452
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.452
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.452
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.452
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.451
1udaUFGUDP-glucose 4-epimerase5.1.3.20.451
2vwqNAPGlucose 1-dehydrogenase/0.451
3hl0NADMaleylacetate reductase/0.451
3tjzGNPADP-ribosylation factor 1/0.451
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.451
4eb7PLPCysteine desulfurase IscS 2/0.451
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.451
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1w6hTITPlasmepsin-23.4.23.390.450
4g3jVNTLanosterol 14-alpha-demethylase/0.450
4ipw1G7Mycocyclosin synthase1.14.21.90.450
4m83ERYOleandomycin glycosyltransferase2.4.10.450
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.450
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.449
1llqNADNAD-dependent malic enzyme, mitochondrial1.1.1.380.449
4xguADPPutative pachytene checkpoint protein 2/0.449
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.448
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.448
2he5NDPAldo-keto reductase family 1 member C211.1.10.448
1o6zNADMalate dehydrogenase/0.447
2gv8NDPThiol-specific monooxygenase1.14.130.447
4acuQN7Beta-secretase 13.4.23.460.446
1fy7COAHistone acetyltransferase ESA1/0.445
2dc1NADProbable L-aspartate dehydrogenase/0.445
3c1y2BADNA integrity scanning protein DisA/0.445
4bfvZVVPantothenate kinase2.7.1.330.445
4nbwNADShort-chain dehydrogenase/reductase SDR/0.445
1tqf32PBeta-secretase 13.4.23.460.444
2a92NAIL-lactate dehydrogenase/0.444
4bfzZVZPantothenate kinase2.7.1.330.444
4g7gVFVLanosterol 14-alpha-demethylase/0.444
3d3wNAPL-xylulose reductase1.1.1.100.443
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.443
4loi1YCStimulator of interferon genes protein/0.443
1lbcCYZGlutamate receptor 2/0.442
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.442
2gz7D3FOrf1a polyprotein/0.442
2i7pACOPantothenate kinase 32.7.1.330.442
2iyfERYOleandomycin glycosyltransferase2.4.10.442
2iypNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.442
3bbrBHYGlutamate receptor 2/0.442
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.442
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.442
3gwfNAPCyclohexanone monooxygenase/0.441
4m4922YL-lactate dehydrogenase A chain1.1.1.270.441
4rvgTYDD-mycarose 3-C-methyltransferase/0.441
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.441
1mjaCOAHistone acetyltransferase ESA1/0.440
2g8yNADHydroxycarboxylate dehydrogenase B/0.440
2y0mACOHistone acetyltransferase KAT8/0.440
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.440
4a862ANMajor pollen allergen Bet v 1-A/0.440
4p63NADProbable deoxyhypusine synthase2.5.1.460.440