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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
4dptAGSMevalonate diphosphate decarboxylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4dptAGSMevalonate diphosphate decarboxylase/1.000
3qt62P0Mevalonate diphosphate decarboxylase/0.586
4dpuAGSMevalonate diphosphate decarboxylase/0.548
4fxy0W2Neurolysin, mitochondrial3.4.24.160.485
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.484
3bk2U5PRibonuclease J/0.480
1xvaSAMGlycine N-methyltransferase2.1.1.200.479
3q43D66M1 family aminopeptidase3.4.110.478
4dpy2P0Mevalonate diphosphate decarboxylase/0.477
3lqfNADGalactitol dehydrogenase/0.471
4du82P0Mevalonate diphosphate decarboxylase/0.471
1xe65FPPlasmepsin-23.4.23.390.469
2rlcCHDCholoylglycine hydrolase3.5.1.240.469
1rftPXMPyridoxal kinase2.7.1.350.468
1xddAAYIntegrin alpha-L/0.466
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.464
1a8rGTPGTP cyclohydrolase 13.5.4.160.462
3bgbLJGGag-Pol polyprotein3.4.23.160.462
4a6bQG8Gag-Pol polyprotein3.4.23.160.461
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.460
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.459
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.455
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.454
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.454
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.454
4bfzZVZPantothenate kinase2.7.1.330.454
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.454
1psa0ZLPepsin A3.4.23.10.453
2b53D23Cyclin-dependent kinase 22.7.11.220.453
2oapANPType II secretion system protein (GspE-2)/0.453
4yaw2AMNADPH--cytochrome P450 reductase/0.453
2a94AP0L-lactate dehydrogenase1.1.1.270.452
2vwqNAPGlucose 1-dehydrogenase/0.452
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4k6fNAPPutative Acetoacetyl-CoA reductase/0.452
4lcjNADC-terminal-binding protein 2/0.452
1sq5ADPPantothenate kinase2.7.1.330.451
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.451
3f3sNADLambda-crystallin homolog/0.451
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.451
1mjaCOAHistone acetyltransferase ESA1/0.450
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.450
3hyoADPPyridoxal kinase/0.450
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.450
3v2uATPProtein GAL3/0.449
4i1iNADMalate dehydrogenase/0.449
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.448
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.448
3h3t16HCollagen type IV alpha-3-binding protein/0.448
3vyfVYFRenin3.4.23.150.448
2vouFAD2,6-dihydroxypyridine 3-monooxygenase1.14.13.100.447
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.447
1fy7COAHistone acetyltransferase ESA1/0.446
1p31EPUUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.446
1udbUFGUDP-glucose 4-epimerase5.1.3.20.446
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.446
1ex75GPGuanylate kinase2.7.4.80.445
1hncGDNGlutathione S-transferase Mu 22.5.1.180.445
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.445
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.444
2gjlFMNNitronate monooxygenase1.13.12.160.444
2qimZEAClass 10 plant pathogenesis-related protein/0.444
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.444
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.444
3tjzGNPADP-ribosylation factor 1/0.444
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.444
4q0kGA3Phytohormone-binding protein/0.444
4wriOKAOkadaic acid binding protein 2-alpha/0.444
2a7r5GPGMP reductase 2/0.443
2b4rAESGlyceraldehyde-3-phosphate dehydrogenase/0.443
2yj5ATPCopper-transporting ATPase/0.443
3c212BADNA integrity scanning protein DisA/0.443
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.443
3h3r14HCollagen type IV alpha-3-binding protein/0.443
5ftfADPTPR domain protein/0.443
1f8wFADNADH peroxidase1.11.1.10.442
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.442
2dftADPShikimate kinase2.7.1.710.442
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.442
3own3OWRenin3.4.23.150.442
4a6cQG9Gag-Pol polyprotein3.4.23.160.442
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.442
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.442
4lutDCSAlanine racemase/0.442
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.441
1p9wANPType II secretion system protein E/0.441
1rneC60Renin3.4.23.150.441
3a3gDLZLumazine protein/0.441
4a802ANMajor pollen allergen Bet v 1-A/0.441
1eq2NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.440
1w6hTITPlasmepsin-23.4.23.390.440
2fdpFRPBeta-secretase 13.4.23.460.440
2ien017Gag-Pol polyprotein3.4.23.160.440
4a83DXCMajor pollen allergen Bet v 1-A/0.440
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.440