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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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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
3lbiGNPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3lbiGNPGTPase HRas/1.000
3lbhGNPGTPase HRas/0.864
4dltGNPGTPase HRas/0.818
3rs4GNPGTPase HRas/0.816
3lbnGNPGTPase HRas/0.766
3k8yGNPGTPase HRas/0.730
4g0nGNPGTPase HRas/0.706
4dsnGCPGTPase KRas/0.696
4hdoGNPRas-related protein Rap-1b/0.684
3v4fGNPGTPase HRas/0.679
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.672
4dlwGNPGTPase HRas/0.666
3l8yGNPGTPase HRas/0.664
3pitGNPRas-related protein M-Ras/0.664
2c5lGTPGTPase HRas/0.663
3i3sGNPGTPase HRas/0.649
3rslGNPGTPase HRas/0.648
3ddcGNPGTPase HRas/0.646
3oiuGNPGTPase HRas/0.641
4l9wGNPGTPase HRas/0.636
3oiwGNPGTPase HRas/0.635
3a58GNPGTP-binding protein RHO1/0.631
3rs0GNPGTPase HRas/0.628
3kkoGNPRas-related protein M-Ras/0.627
5b2zGNPGTPase HRas/0.627
4rkfGNPRas-related protein Rab-3/0.626
3x1zGNPRas-related protein Rap-1b/0.621
2rgeGNPGTPase HRas/0.616
3e5hGNPRas-related protein Rab-28/0.613
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.611
4nyjGNPGTPase HRas/0.609
1xtsGTPGTP-binding protein Rheb/0.607
3a6pGTPGTP-binding nuclear protein Ran/0.607
4nyiGNPGTPase HRas/0.606
3oesGNPGTPase RhebL1/0.605
1zbdGTPRas-related protein Rab-3A/0.604
1e96GTPRas-related C3 botulinum toxin substrate 1/0.603
3rabGNPRas-related protein Rab-3A/0.603
4l9sGDPGTPase HRas/0.600
5difGNPGTP-binding nuclear protein Ran/0.598
1a2bGSPTransforming protein RhoA/0.597
1kmqGNPTransforming protein RhoA/0.596
3rs7GNPGTPase HRas/0.595
4mitGTPRho-related protein racC/0.595
5dhaGNPGTP-binding nuclear protein Ran/0.593
1t91GTPRas-related protein Rab-7a/0.592
1yzqGNPRas-related protein Rab-6A/0.592
4dlzGNPGTPase HRas/0.592
2rgcGNPGTPase HRas/0.590
3kucGDPRas-related protein Rap-1A/0.586
4qxaGTPRas-related protein Rab-9A/0.584
1g17GNPRas-related protein SEC4/0.581
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.581
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.581
2rggGNPGTPase HRas/0.581
3kudGDPGTPase HRas/0.580
1cxzGSPTransforming protein RhoA/0.579
2gcpGSPRho-related GTP-binding protein RhoC/0.579
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.578
3tgpGNPGTPase HRas/0.577
3wyfGTPGTP-binding nuclear protein/0.572
1zc4GNPRas-related protein Ral-A/0.570
2rgbGNPGTPase HRas/0.570
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.569
4dlsGNPGTPase HRas/0.567
4lhwGNPRas-related protein Rab-8A/0.567
4l8gGDPGTPase KRas/0.566
4o2lGTPGTP-binding protein Rheb/0.566
1ibrGNPGTP-binding nuclear protein Ran/0.564
3bbpGTPRas-related protein Rab-6A/0.564
3w3zGTPGTP-binding nuclear protein Ran/0.564
4hdqGNPRas-related protein Rap-1b/0.564
5jljGNPGTP-binding nuclear protein Ran/0.564
4tq9GDPGTPase KRas/0.563
4xvrGNPGTPase HRas/0.561
3k9lGNPGTPase HRas/0.560
4kvgGTPRas-related protein Rap-1A/0.560
1xtrGNPGTP-binding protein Rheb/0.559
1yu9GNPRas-related protein Rab-4A/0.557
3th5GNPRas-related C3 botulinum toxin substrate 1/0.557
1n6lGTPRas-related protein Rab-5A/0.555
1zc3GNPRas-related protein Ral-A/0.554
4epwGDPGTPase KRas/0.553
2fe4GDPRas-related protein Rab-6B/0.551
1m7bGTPRho-related GTP-binding protein RhoE/0.550
3oivGNPGTPase HRas/0.550
3tsoGNPRas-related protein Rab-25/0.549
4lpkGDPGTPase KRas/0.549
3nbzGTPGTP-binding nuclear protein Ran/0.548
4wa7GDPGTPase KRas/0.548
2bkuGTPGTP-binding nuclear protein Ran/0.545
4o25GTPGTP-binding protein Rheb/0.542
3ea5GDPGTP-binding nuclear protein Ran/0.541
4obeGDPGTPase KRas/0.540
1zd9GDPADP-ribosylation factor-like protein 8A/0.538
4q03GDPGTPase KRas/0.538
4dlxGNPGTPase HRas/0.536
4epxGDPGTPase KRas/0.536
3rs5GNPGTPase HRas/0.534
4lrwGDPGTPase KRas/0.532
3qbtGNPRas-related protein Rab-8A/0.531
1vg8GNPRas-related protein Rab-7a/0.530
1yhnGTPRas-related protein Rab-7a/0.529
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.528
1gwnGTPRho-related GTP-binding protein RhoE/0.527
4ol0GTPGTP-binding nuclear protein Ran/0.527
3eg5GNPCell division control protein 42 homolog/0.525
4lv6GDPGTPase KRas/0.525
3cphGDPRas-related protein SEC4/0.522
2ce2GDPGTPase HRas/0.520
1x1rGDPRas-related protein M-Ras/0.519
3kz1GSPTransforming protein RhoA/0.519
4dsoGSPGTPase KRas/0.519
4js0GNPCell division control protein 42 homolog/0.519
4ql3GDPGTPase KRas/0.519
4xvqGNPGTPase HRas/0.519
2ffqGSPRas-related protein Rab-6B/0.517
2msdGNPMHC class I alpha chain/0.516
4q02GDPGTPase KRas/0.516
1lfdGNPGTPase HRas/0.515
2bmeGNPRas-related protein Rab-4A/0.515
4dlvGNPGTPase HRas/0.514
1d5cGDPGTPase (Rab6)/0.512
4uj3GNPRas-related protein Rab-11A/0.511
4cidANPEH domain-containing protein 2/0.510
4g2i0VQVitamin D3 receptor/0.510
4ldjGDPGTPase KRas/0.510
4o2rGDPGTP-binding protein Rheb/0.506
2cl6CAGGTPase HRas/0.504
1z2aGDPRas-related protein Rab-23/0.503
2fg5GNPRas-related protein Rab-31/0.503
3kkqGDPRas-related protein M-Ras/0.503
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.503
1oixGDPRas-related protein Rab-11A/0.502
1k5dGNPGTP-binding nuclear protein Ran/0.501
2o4jVD4Vitamin D3 receptor/0.498
5hpyGDPTransforming protein RhoA/0.492
2hb7O1CVitamin D3 receptor/0.491
2q3fGNPRas-related GTP-binding protein D/0.491
1z0dGDPRas-related protein Rab-5C/0.490
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.489
4uj5GNPRas-related protein Rab-11A/0.487
3w5tLHPVitamin D3 receptor/0.486
2o4rVD5Vitamin D3 receptor/0.485
1z2cGNPRho-related GTP-binding protein RhoC/0.484
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.483
1v8kANPKinesin-like protein KIF2C/0.483
2clsGTPRho-related GTP-binding protein Rho6/0.483
1ky2GNPGTP-binding protein YPT7/0.482
1ow3GDPTransforming protein RhoA/0.482
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.480
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.479
2zlcVDXVitamin D3 receptor/0.478
3x1wGDPRas-related protein Rap-1b/0.478
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.477
3vrvYSDVitamin D3 receptor/0.476
2mscGDPMHC class I alpha chain/0.475
2mseGNPMHC class I alpha chain/0.475
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.475
3gy9COAGCN5-related N-acetyltransferase/0.474
4ia7BIVVitamin D3 receptor A/0.474
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.473
3w0c6DSVitamin D3 receptor/0.473
3a783EVVitamin D3 receptor/0.472
1rkgVD1Vitamin D3 receptor/0.470
3fvqATPFe(3+) ions import ATP-binding protein FbpC/0.469
3w0jT08Vitamin D3 receptor/0.469
3pzcCOAAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.468
1m2oGNPSmall COPII coat GTPase SAR13.6.50.467
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.467
2wu5CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.467
2wu5CBESuccinate dehydrogenase cytochrome b556 subunit/0.467
4d0lGSPRas-related protein Rab-11A/0.467
4itfTFYVitamin D3 receptor/0.467
2hb8MVDVitamin D3 receptor/0.466
2xvv9DNSerum albumin/0.466
4g1y0VOVitamin D3 receptor A/0.466
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.466
1ay0TPPTransketolase 12.2.1.10.465
1rd4L08Integrin alpha-L/0.465
2hamC33Vitamin D3 receptor/0.465
3x03ANPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.465
4fhi0S4Vitamin D3 receptor A/0.465
4mv3ACPBiotin carboxylase6.3.4.140.465
2dw4FADLysine-specific histone demethylase 1A10.464
2zl9VDAVitamin D3 receptor/0.464
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.464
4rupH97Vitamin D3 receptor A/0.464
3kpzZNEVitamin D3 receptor/0.463
3vhxGTPADP-ribosylation factor 6/0.463
4q0a4OAVitamin D3 receptor A/0.463
1e0jANPDNA primase/helicase2.7.70.462
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.462
4g1d0VKVitamin D3 receptor A/0.462
4lzwTHMUridine phosphorylase/0.462
3gyaCOAGCN5-related N-acetyltransferase/0.461
3m7rVDXVitamin D3 receptor/0.461
1s19MC9Vitamin D3 receptor/0.460
2j0vGDPRac-like GTP-binding protein ARAC7/0.460
1rx8FOLDihydrofolate reductase1.5.1.30.459
4gojGNPADP-ribosylation factor-like protein 3/0.458
5ab6CAANonspecific lipid-transfer protein, putative/0.458
3jq3ADPLombricine kinase/0.457
4buv16ITankyrase-22.4.2.300.457
4edz0O5Hematopoietic prostaglandin D synthase/0.457
1wdtGTPElongation factor G (EF-G-2)/0.456
3ddw055Glycogen phosphorylase, liver form2.4.1.10.456
3x04GNPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.456
4bfvZVVPantothenate kinase2.7.1.330.456
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.455
2bxqIMNSerum albumin/0.455
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.455
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.455
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.454
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.454
4ead0NPThymidine phosphorylase2.4.2.40.454
2zlaVDBVitamin D3 receptor/0.453
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.453
3fr28CAFatty acid-binding protein, adipocyte/0.453
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.453
5iotUMPFlavin-dependent thymidylate synthase2.1.1.1480.453
1rx8NAPDihydrofolate reductase1.5.1.30.452
2a9z26AAdenosine kinase2.7.1.200.452
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.452
4m11MXMProstaglandin G/H synthase 21.14.99.10.451
1bcpATPPertussis toxin subunit 4/0.450
1bcpATPPertussis toxin subunit 5/0.450
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.450
4nu6NADPhosphonate dehydrogenase1.20.1.10.450
4uy6SAHHistidine N-alpha-methyltransferase/0.450
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.449
3refGDPRho family GTPase/0.449
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.448
3w0yDS4Vitamin D3 receptor/0.448
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.448
1dj3GDPAdenylosuccinate synthetase, chloroplastic/0.447
1tu3GNPRas-related protein Rab-5A/0.447
2bx8AZQSerum albumin/0.447
2z1mGDPGDP-mannose 4,6-dehydratase/0.447
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.447
4ia1BIVVitamin D3 receptor A/0.447
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.446
3cobADPKinesin heavy chain-like protein/0.446
4b3aTACTetracycline repressor protein class D/0.446
4dvgGSPRho family GTPase/0.446
4la7A1OAbscisic acid receptor PYL2/0.446
4xymCOAAcyl-CoA synthetase (NDP forming)/0.446
2y1xSAHHistone-arginine methyltransferase CARM1/0.445
3pcrGTPADP-ribosylation factor 6/0.445
3ujlA8SAbscisic acid receptor PYL2/0.445
2zbaZBATrichothecene 3-O-acetyltransferase/0.444
3dolGWIPol protein/0.444
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3nga3NGCasein kinase II subunit alpha2.7.11.10.444
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.444
3pqbVGPPutative oxidoreductase/0.444
1bim0QBRenin3.4.23.150.443
3jziJZLBiotin carboxylase6.3.4.140.443
3naxMP73-phosphoinositide-dependent protein kinase 12.7.11.10.443
3qfcNAPNADPH--cytochrome P450 reductase/0.443
4dc0NDPPutative ketoacyl reductase1.3.10.443
4ymkST9Acyl-CoA desaturase 1/0.443
4z34ON7Lysophosphatidic acid receptor 1/0.443
1e7aPFLSerum albumin/0.442
1ve3SAMUncharacterized protein/0.442
3ukrCKHActin-related protein 3/0.442
3ukrCKHActin-related protein 2/0.442
3up0D7SaceDAF-12/0.442
3v1s0LHStrictosidine synthase4.3.3.20.442
3wqtANPCell division protein FtsA/0.442
2a9y26AAdenosine kinase2.7.1.200.441
2bc9GNPGuanylate-binding protein 1/0.441
2j5sKTAAlr4455 protein/0.441
2p1u4TNRetinoic acid receptor RXR-alpha/0.441
2x06NADL-sulfolactate dehydrogenase/0.441
2xauADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP433.6.4.130.441
4hl1ZZ7Metallo-beta-lactamase type 2/0.441
4ia3BIVVitamin D3 receptor A/0.441
4iwyADPRibosomal protein S6--L-glutamate ligase/0.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
4rkdKETAminotransferase/0.441
1ndzFR5Adenosine deaminase3.5.4.40.440
1r2jFADFkbI/0.440
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2hbhXE4Vitamin D3 receptor A/0.440
2ohjFMNType A flavoprotein FprA10.440
3dvlATPCircadian clock protein kinase KaiC2.7.11.10.440
3x065GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.440
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.440
5kf1COAPredicted acetyltransferase/0.440