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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
3is2FADVivid PAS protein VVD

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3is2FADVivid PAS protein VVD/1.000
3d72FADVivid PAS protein VVD/0.733
2pd8FADVivid PAS protein VVD/0.683
3hjiFADVivid PAS protein VVD/0.629
3hjkFADVivid PAS protein VVD/0.608
2pd7FADVivid PAS protein VVD/0.600
2pdtFADVivid PAS protein VVD/0.583
4wujFMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy/0.575
4r38RBFBlue-light-activated histidine kinase 22.7.13.30.568
2z6dFMNPhototropin-22.7.11.10.563
1n9nFMNPutative blue light receptor/0.556
3p7nFMNLight-activated DNA-binding protein EL222/0.552
1n9lFMNPutative blue light receptor/0.534
4hhdFMNPhototropin-12.7.11.10.532
4eetFMNPhototropin-22.7.11.10.531
5djtFMNNPH1-2/0.528
2pr5FMNBlue-light photoreceptor/0.519
5dkkFMNPredicted protein/0.510
3sw1FMNSensory box protein/0.509
3t50FMNBlue-light-activated histidine kinase2.7.13.30.506
4eeuFMNPhototropin-22.7.11.10.501
5djuFMNNPH1-2/0.499
2p4yC03Peroxisome proliferator-activated receptor gamma/0.497
4kukRBFPutative blue-light photoreceptor/0.491
4ji91M3Tyrosine-protein kinase JAK2/0.487
4hj4FMNLOV protein/0.486
1pnvTYDdTDP-epi-vancosaminyltransferase2.4.1.3110.484
2z6cFMNPhototropin-12.7.11.10.483
4hiaFMNLOV protein/0.480
4xj3GTPCyclic GMP-AMP synthase/0.480
4kuoRBFPutative blue-light photoreceptor/0.479
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.477
2q59240Peroxisome proliferator-activated receptor gamma/0.475
3ibqATPPyridoxal kinase/0.475
5cnnANPEpidermal growth factor receptor2.7.10.10.475
4eerFMNPhototropin-22.7.11.10.474
4eesFMNPhototropin-22.7.11.10.473
4jy2FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.473
4deeADPAurora kinase A2.7.11.10.472
5cnoANPEpidermal growth factor receptor2.7.10.10.472
5dpvSKEAurora kinase A2.7.11.10.472
4hj6FMNLOV protein/0.471
5efwFMNNPH1-1/0.471
2he5NDPAldo-keto reductase family 1 member C211.1.10.469
4a4vYFDPeroxisome proliferator-activated receptor gamma/0.469
2q54MU1Protease/0.467
3t1tGDPProbable gliding protein mglA/0.465
2cig1DGDihydrofolate reductase1.5.1.30.464
3ub5ATPActin, cytoplasmic 1/0.464
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.464
3f3sNADLambda-crystallin homolog/0.463
1qvrANPChaperone protein ClpB/0.462
3ue6FMNAureochrome1/0.462
2q631UNGag-Pol polyprotein3.4.23.160.461
4jjiNADAlcohol dehydrogenase class-3/0.461
1udaUFGUDP-glucose 4-epimerase5.1.3.20.460
2q61SF1Peroxisome proliferator-activated receptor gamma/0.460
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.459
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.459
2pym1UNGag-Pol polyprotein3.4.23.160.457
3t99ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.457
1rywEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.456
3hyoADPPyridoxal kinase/0.455
4fxfATPPyruvate kinase PKM2.7.1.400.455
1hxbROCGag-Pol polyprotein3.4.23.160.454
3icsCOACoenzyme A disulfide reductase/0.454
4hnbFMNLOV protein/0.454
4xumIMNPeroxisome proliferator-activated receptor gamma/0.454
3bc3OPTCathepsin L13.4.22.150.453
3cs8BRLPeroxisome proliferator-activated receptor gamma/0.453
4lj9ACPChaperone protein ClpB/0.453
5jlaNADPutative short-chain dehydrogenase/reductase/0.453
1a5uATPPyruvate kinase PKM2.7.1.400.452
1l8qADPChromosomal replication initiator protein DnaA/0.452
4u03GTPCyclic GMP-AMP synthase/0.452
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.452
2gjlFMNNitronate monooxygenase1.13.12.160.451
2q5p241Peroxisome proliferator-activated receptor gamma/0.451
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.451
4guvFADTetX family tetracycline inactivation enzyme/0.451
1pn3TYDdTDP-epi-vancosaminyltransferase2.4.1.3110.450
2mwgFMNBlue-light photoreceptor/0.450
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.450
3i6oGR6Gag-Pol polyprotein3.4.23.160.450
3icrCOACoenzyme A disulfide reductase/0.450
4nmdFDABifunctional protein PutA/0.450
4r3aRBFBlue-light-activated histidine kinase 22.7.13.30.450
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.449
3r1kCOAN-acetyltransferase Eis/0.449
3vf7031Gag-Pol polyprotein3.4.23.160.448
4kl9NDPDihydrofolate reductase1.5.1.30.448
4lxhC1EAlpha/beta hydrolase fold/0.448
2q29ACOOxalyl-CoA decarboxylase4.1.1.80.447
3qqs17CAnthranilate phosphoribosyltransferase/0.447
3t9aANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.447
4fuyEK2Mitogen-activated protein kinase 12.7.11.240.447
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.446
1yb5NAPQuinone oxidoreductase1.6.5.50.446
2p33J07Mitogen-activated protein kinase 102.7.11.240.446
2qi6MZ8Gag-Pol polyprotein/0.446
3ik6HCZGlutamate receptor 2/0.446
4qnyANPMitogen activated protein kinase, putative/0.446
4r7uUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.446
1b16NAQAlcohol dehydrogenase1.1.1.10.445
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.445
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.445
3triNAPPyrroline-5-carboxylate reductase/0.445
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.445
4n9iPCGCatabolite expression activator/0.445
1bdrIM1Gag-Pol polyprotein3.4.23.160.444
1dg8NDPDihydrofolate reductase1.5.1.30.444
2a94AP0L-lactate dehydrogenase1.1.1.270.444
2d1cNAPIsocitrate dehydrogenase [NADP]1.1.1.420.444
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.444
3b9lAZZSerum albumin/0.444
3t14FADSulfide-quinone reductase/0.444
3wfjNAD2-dehydropantoate 2-reductase/0.444
4cukNAID-lactate dehydrogenase/0.444
1zeoC01Peroxisome proliferator-activated receptor gamma/0.443
2uxpCLMHTH-type transcriptional regulator TtgR/0.443
2y4gTIRTamL/0.443
3ad9NADSubunit alpha of sarocosine oxidase/0.443
3ekx1UNGag-Pol polyprotein3.4.23.160.443
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.443
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.442
2q5g1FAPeroxisome proliferator-activated receptor delta/0.442
3bva2NCGag-Pol polyprotein3.4.23.160.442
3i7eDJRGag-Pol polyprotein/0.442
3inmNDPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.442
3lqfNADGalactitol dehydrogenase/0.442
3wdlATP4-phosphopantoate--beta-alanine ligase6.3.2.360.442
4eepFMNPhototropin-22.7.11.10.442
4ku2MYA3-oxoacyl-[ACP] synthase III/0.442
4yswFADXanthine dehydrogenase/oxidase/0.442
1a72PADAlcohol dehydrogenase E chain1.1.1.10.441
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.441
1ykdCMPAdenylate cyclase/0.441
2q5kAB1Protease/0.441
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.441
3ecg065Gag-Pol polyprotein3.4.23.470.441
4rpgFADUDP-galactopyranose mutase5.4.99.90.441
1juvNDPDihydrofolate reductase1.5.1.30.440
2ejvNADL-threonine 3-dehydrogenase/0.440
2gqrADPPhosphoribosylaminoimidazole-succinocarboxamide synthase6.3.2.60.440
2hs1017Protease/0.440
2izrBRKCasein kinase I isoform gamma-32.7.11.10.440
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.440
3el01UNGag-Pol polyprotein3.4.23.160.440
3el4ROCGag-Pol polyprotein3.4.23.160.440
3t9fADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.440
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.440
4q73FADBifunctional protein PutA/0.440