Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/1.000
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.755
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.677
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.638
2a94AP0L-lactate dehydrogenase1.1.1.270.570
3gviADPMalate dehydrogenase/0.544
1t2cNAIL-lactate dehydrogenase1.1.1.270.542
2a92NAIL-lactate dehydrogenase/0.538
4rosAPRMalate dehydrogenase/0.531
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.528
3gvhNADMalate dehydrogenase/0.525
1guyNADMalate dehydrogenase/0.510
1ur5NADMalate dehydrogenase/0.507
4k28NADShikimate dehydrogenase family protein/0.507
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.506
1uxjNADMalate dehydrogenase/0.505
1pzhNADLactate dehydrogenase/0.504
1uxkNADMalate dehydrogenase/0.502
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.496
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.496
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.494
2hfuMEVMevalonate kinase/0.494
4nbwNADShort-chain dehydrogenase/reductase SDR/0.493
1ie3NADMalate dehydrogenase/0.486
1pzfA3DLactate dehydrogenase/0.485
2gjnFMNNitronate monooxygenase1.13.12.160.485
3lqfNADGalactitol dehydrogenase/0.484
4egbNADdTDP-glucose 4,6-dehydratase/0.482
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.481
3b70NAPEnoyl reductase LovC10.480
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.480
4q71FADBifunctional protein PutA/0.480
1h50FMNPentaerythritol tetranitrate reductase/0.478
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.478
4lcjNADC-terminal-binding protein 2/0.478
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.477
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.476
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.476
1pjcNADAlanine dehydrogenase/0.475
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.474
4jicFMNGTN Reductase/0.474
5mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.474
4fncHMUG/T mismatch-specific thymine DNA glycosylase3.2.2.290.473
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.472
4ktkKTKCytochrome P450/0.472
5a3bAPRSIR2 family protein/0.472
2g247IGRenin3.4.23.150.471
2i4qUA4Renin3.4.23.150.471
4l4sNAIL-lactate dehydrogenase A chain1.1.1.270.471
1xe65FPPlasmepsin-23.4.23.390.470
2givACOHistone acetyltransferase KAT8/0.470
3drcMTXDihydrofolate reductase1.5.1.30.470
3to6LYS_CMCHistone acetyltransferase ESA1/0.470
2g1o2IGRenin3.4.23.150.468
2g226IGRenin3.4.23.150.468
3ekuCY9Actin-5C/0.468
3qlsNDPDihydrofolate reductase1.5.1.30.468
3r9uFADThioredoxin reductase/0.468
1g1aNADdTDP-glucose 4,6-dehydratase/0.467
2a7r5GPGMP reductase 2/0.467
3p62FMNPentaerythritol tetranitrate reductase/0.467
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.467
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.466
1rneC60Renin3.4.23.150.466
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.466
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.466
4m6jNDPDihydrofolate reductase1.5.1.30.466
2gjlFMNNitronate monooxygenase1.13.12.160.465
4i1iNADMalate dehydrogenase/0.465
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.465
4tuvCPZCytochrome P450 1191.140.465
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.465
1npdNADQuinate/shikimate dehydrogenase/0.464
3b6zCO7Enoyl reductase LovC10.464
4a862ANMajor pollen allergen Bet v 1-A/0.464
4e2dFMNDehydrogenase/0.463
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.462
2abbFMNPentaerythritol tetranitrate reductase/0.462
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.462
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
2ejvNADL-threonine 3-dehydrogenase/0.461
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.461
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.461
1lbcCYZGlutamate receptor 2/0.460
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
4blsAPCNTPase P4/0.460
2dc1NADProbable L-aspartate dehydrogenase/0.459
4dbzNDPPutative ketoacyl reductase1.3.10.459
2qbuSAHPrecorrin-2 methyltransferase/0.458
2y0mACOHistone acetyltransferase KAT8/0.458
3atzFMNProstaglandin F2a synthase/0.458
3h3jNADL-lactate dehydrogenase 11.1.1.270.458
3mknDNBPyrimidine-specific ribonucleoside hydrolase RihB/0.458
3tjzGNPADP-ribosylation factor 1/0.458
4dc0NDPPutative ketoacyl reductase1.3.10.458
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.458
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.458
1emdNADMalate dehydrogenase/0.457
2omeNADC-terminal-binding protein 2/0.457
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.457
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.457
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.456
2vbdV10Isopenicillin N synthase1.21.3.10.456
3vsxR32Renin3.4.23.150.456
4q0kGA3Phytohormone-binding protein/0.456
4udrFAD5-(hydroxymethyl)furfural oxidase/0.456
1mj9COAHistone acetyltransferase ESA1/0.455
1xe55FEPlasmepsin-23.4.23.390.455
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.455
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.455
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.455
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.455
2rcyNAPPyrroline-5-carboxylate reductase/0.455
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.455
3a3gDLZLumazine protein/0.455
3vyfVYFRenin3.4.23.150.455
4g2gTDHMycocyclosin synthase1.14.21.90.455
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1nytNAPShikimate dehydrogenase (NADP(+))/0.454
1ra8FOLDihydrofolate reductase1.5.1.30.454
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.454
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.454
3gqvNAPEnoyl reductase LovC10.454
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.454
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.454
4g47TZFMycocyclosin synthase1.14.21.90.454
4g95OAGDihydrofolate reductase1.5.1.30.454
4k81GTPGTPase HRas/0.454
4q73FADBifunctional protein PutA/0.454
1bwlFMNNADPH dehydrogenase 11.6.99.10.453
1dyiFOLDihydrofolate reductase1.5.1.30.453
1h63FMNPentaerythritol tetranitrate reductase/0.453
1o9bNAIQuinate/shikimate dehydrogenase/0.453
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.453
3d3wNAPL-xylulose reductase1.1.1.100.453
1ddrMTXDihydrofolate reductase1.5.1.30.452
1nvtNAPShikimate dehydrogenase (NADP(+))/0.452
2p5uNADUDP-glucose 4-epimerase/0.452
3oafOAGDihydrofolate reductase1.5.1.30.452
3s1dZIRCytokinin dehydrogenase 11.5.99.120.452
4eb7PLPCysteine desulfurase IscS 2/0.452
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.452
5fwnNAPPutative dehydrogenase/0.452
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.451
1me6IVSPlasmepsin-23.4.23.390.451
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.451
3btsNADGalactose/lactose metabolism regulatory protein GAL80/0.451
4a8v2ANMajor pollen allergen Bet v 1-J/0.451
4m83ERYOleandomycin glycosyltransferase2.4.10.451
2g1r3IGRenin3.4.23.150.450
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.450
2ylrNAPPhenylacetone monooxygenase1.14.13.920.450
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3toxNAPPutative oxidoreductase/0.450
4a86H35Major pollen allergen Bet v 1-A/0.450
4eu8COASuccinyl-CoA:acetate CoA-transferase/0.450
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.450
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.449
1h73ANPHomoserine kinase2.7.1.390.449
1ia1NDPDihydrofolate reductase1.5.1.30.449
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.449
2ath3EAPeroxisome proliferator-activated receptor gamma/0.449
2zvbSAHPrecorrin-3 C17-methyltransferase/0.449
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3kpbSAMUncharacterized protein MJ0100/0.449
4ambDUDPutative glycosyl transferase/0.449
4g7gVFVLanosterol 14-alpha-demethylase/0.449
4gavFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.449
4k6fNAPPutative Acetoacetyl-CoA reductase/0.449
1b5eDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.448
1dyjDDFDihydrofolate reductase1.5.1.30.448
1xkdNAPIsocitrate dehydrogenase [NADP]/0.448
3ensENSCoagulation factor X3.4.21.60.448
3f03FMNPentaerythritol tetranitrate reductase/0.448
3qlrNDPDihydrofolate reductase1.5.1.30.448
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.448
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
5a3cNADSIR2 family protein/0.448
1b8uNADMalate dehydrogenase/0.447
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
1xddAAYIntegrin alpha-L/0.447
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.447
2qbmCAMCamphor 5-monooxygenase1.14.15.10.447
3gfbNADL-threonine 3-dehydrogenase/0.447
3mk6ACOPantothenate kinase 32.7.1.330.447
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.447
4ajo88NL-lactate dehydrogenase A chain1.1.1.270.447
4bfvZVVPantothenate kinase2.7.1.330.447
4hwkNAPSepiapterin reductase1.1.1.1530.447
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.447
1eioGCHGastrotropin/0.446
1hyhNADL-2-hydroxyisocaproate dehydrogenase/0.446
1nzdUPGDNA beta-glucosyltransferase/0.446
1u3dFADCryptochrome-1/0.446
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.446
2c29NAPDihydroflavonol 4-reductase/0.446
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.446
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.446
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.446
3nsh957Beta-secretase 13.4.23.460.446
3uylTYDProbable NDP-rhamnosyltransferase/0.446
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.446
4i0i957Beta-secretase 13.4.23.460.446
1udbUFGUDP-glucose 4-epimerase5.1.3.20.445
2il2LIXRenin3.4.23.150.445
2nniMTKCytochrome P450 2C8/0.445
2ohvNHLGlutamate racemase/0.445
2zcvNDPQuinone oxidoreductase 21.6.5.20.445
3i0pNADMalate dehydrogenase, putative/0.445
3lpiZ74Beta-secretase 13.4.23.460.445
3oetNADErythronate-4-phosphate dehydrogenase/0.445
4f4qFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.445
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.445
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.444
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.444
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1mjbACOHistone acetyltransferase ESA1/0.444
1pd9CO4Dihydrofolate reductase1.5.1.30.444
2ft9CHDFatty acid-binding protein 2, liver/0.444
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.444
3cisATPUniversal stress protein Rv2623/0.444
3ieuGDPGTPase Era/0.444
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.444
3mvm39PMitogen-activated protein kinase 14/0.444
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.444
3vyeVYERenin3.4.23.150.444
4fse0VABeta-secretase 13.4.23.460.444
1icsFMN12-oxophytodienoate reductase 11.3.1.420.443
1xvaSAMGlycine N-methyltransferase2.1.1.200.443
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.443
2iko7IGRenin3.4.23.150.443
2rlcCHDCholoylglycine hydrolase3.5.1.240.443
3nxxNDPDihydrofolate reductase1.5.1.30.443
3p82FMNPentaerythritol tetranitrate reductase/0.443
3w1qYRODihydroorotate dehydrogenase (fumarate)1.3.98.10.443
3zeiAWHO-acetylserine sulfhydrylase/0.443
4i02CMPcAMP-activated global transcriptional regulator CRP/0.443
1jolFFODihydrofolate reductase1.5.1.30.442
1sxjAGSReplication factor C subunit 1/0.442
1udaUFGUDP-glucose 4-epimerase5.1.3.20.442
2g1y5IGRenin3.4.23.150.442
2gv8NDPThiol-specific monooxygenase1.14.130.442
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.442
3ai2NDPNADPH-sorbose reductase/0.442
3pw8ACO1,2-phenylacetyl-CoA epoxidase, subunit A1.14.13.1490.442
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
3w8eNAD3-hydroxybutyrate dehydrogenase/0.442
4dfg0JVGag-Pol polyprotein3.4.23.160.442
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
5bsgNAPPyrroline-5-carboxylate reductase/0.442
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.441
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.441
1vi2NADQuinate/shikimate dehydrogenase/0.441
2b53D23Cyclin-dependent kinase 22.7.11.220.441
2briANPUridylate kinase2.7.4.220.441
2zb3NDPProstaglandin reductase 21.3.1.480.441
3atyFMNProstaglandin F2a synthase/0.441
3bg7FADPyranose 2-oxidase/0.441
3d4pNADL-lactate dehydrogenase 11.1.1.270.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3exo5MSBeta-secretase 13.4.23.460.441
4ajj88RL-lactate dehydrogenase A chain1.1.1.270.441
4rvnCOAPhenylacetate-coenzyme A ligase/0.441
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.441
4yryFADGlutamate synthase, beta subunit/0.441
5d3qGDPDynamin-13.6.5.50.441
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.440
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.440
1fy7COAHistone acetyltransferase ESA1/0.440
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
1kfbIGPTryptophan synthase alpha chain/0.440
2ien017Gag-Pol polyprotein3.4.23.160.440
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.440
2x0iNAIMalate dehydrogenase/0.440
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
3nmpPYVAbscisic acid receptor PYL2/0.440
4du82P0Mevalonate diphosphate decarboxylase/0.440
4l4eCAMCamphor 5-monooxygenase1.14.15.10.440