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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
4l9wGNPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4l9wGNPGTPase HRas/1.000
4dlzGNPGTPase HRas/0.706
3rs4GNPGTPase HRas/0.705
4dlxGNPGTPase HRas/0.701
2rgbGNPGTPase HRas/0.696
3rslGNPGTPase HRas/0.690
3lbnGNPGTPase HRas/0.679
3rs0GNPGTPase HRas/0.679
4dlsGNPGTPase HRas/0.677
4dlvGNPGTPase HRas/0.676
3lbiGNPGTPase HRas/0.674
2rgcGNPGTPase HRas/0.672
3l8yGNPGTPase HRas/0.672
3rs7GNPGTPase HRas/0.666
4dltGNPGTPase HRas/0.665
3v4fGNPGTPase HRas/0.660
2rgeGNPGTPase HRas/0.658
4dsnGCPGTPase KRas/0.654
3pitGNPRas-related protein M-Ras/0.653
3oiwGNPGTPase HRas/0.649
2c5lGTPGTPase HRas/0.648
4dlwGNPGTPase HRas/0.647
3lbhGNPGTPase HRas/0.646
3oivGNPGTPase HRas/0.646
4g0nGNPGTPase HRas/0.645
3rs5GNPGTPase HRas/0.640
3kudGDPGTPase HRas/0.638
5b2zGNPGTPase HRas/0.637
1g17GNPRas-related protein SEC4/0.636
5difGNPGTP-binding nuclear protein Ran/0.636
3k8yGNPGTPase HRas/0.633
1e96GTPRas-related C3 botulinum toxin substrate 1/0.632
4hdoGNPRas-related protein Rap-1b/0.627
3i3sGNPGTPase HRas/0.625
3kkoGNPRas-related protein M-Ras/0.625
3a6pGTPGTP-binding nuclear protein Ran/0.622
3e5hGNPRas-related protein Rab-28/0.620
3ddcGNPGTPase HRas/0.618
3a58GNPGTP-binding protein RHO1/0.615
4rkfGNPRas-related protein Rab-3/0.615
3oiuGNPGTPase HRas/0.612
4dsoGSPGTPase KRas/0.610
5dhaGNPGTP-binding nuclear protein Ran/0.609
1zbdGTPRas-related protein Rab-3A/0.608
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.605
3kucGDPRas-related protein Rap-1A/0.604
4lpkGDPGTPase KRas/0.604
3x1zGNPRas-related protein Rap-1b/0.602
4lrwGDPGTPase KRas/0.602
4nyjGNPGTPase HRas/0.598
3w3zGTPGTP-binding nuclear protein Ran/0.590
3ea5GDPGTP-binding nuclear protein Ran/0.588
5jljGNPGTP-binding nuclear protein Ran/0.587
4l8gGDPGTPase KRas/0.586
1t91GTPRas-related protein Rab-7a/0.583
2bkuGTPGTP-binding nuclear protein Ran/0.578
4mitGTPRho-related protein racC/0.575
4hdqGNPRas-related protein Rap-1b/0.572
4lv6GDPGTPase KRas/0.571
4tq9GDPGTPase KRas/0.570
4l9sGDPGTPase HRas/0.569
3bbpGTPRas-related protein Rab-6A/0.564
2fe4GDPRas-related protein Rab-6B/0.563
4o25GTPGTP-binding protein Rheb/0.561
1zd9GDPADP-ribosylation factor-like protein 8A/0.559
1yzqGNPRas-related protein Rab-6A/0.558
1zc3GNPRas-related protein Ral-A/0.556
1cxzGSPTransforming protein RhoA/0.555
1zc4GNPRas-related protein Ral-A/0.554
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.552
4epxGDPGTPase KRas/0.552
4obeGDPGTPase KRas/0.550
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.546
2rggGNPGTPase HRas/0.544
1a2bGSPTransforming protein RhoA/0.543
1k5dGNPGTP-binding nuclear protein Ran/0.542
3kkqGDPRas-related protein M-Ras/0.542
3wyfGTPGTP-binding nuclear protein/0.540
1vg8GNPRas-related protein Rab-7a/0.539
3tgpGNPGTPase HRas/0.538
4epwGDPGTPase KRas/0.537
4o2lGTPGTP-binding protein Rheb/0.537
4q02GDPGTPase KRas/0.536
4xvqGNPGTPase HRas/0.536
4ql3GDPGTPase KRas/0.534
3x1wGDPRas-related protein Rap-1b/0.533
2ffqGSPRas-related protein Rab-6B/0.531
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.531
1m7bGTPRho-related GTP-binding protein RhoE/0.530
1z0dGDPRas-related protein Rab-5C/0.528
4qxaGTPRas-related protein Rab-9A/0.526
2ce2GDPGTPase HRas/0.524
1x1rGDPRas-related protein M-Ras/0.523
4q03GDPGTPase KRas/0.523
2gcpGSPRho-related GTP-binding protein RhoC/0.521
4xvrGNPGTPase HRas/0.521
1n6lGTPRas-related protein Rab-5A/0.519
3k9lGNPGTPase HRas/0.519
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.519
4wa7GDPGTPase KRas/0.519
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.518
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.517
1z2aGDPRas-related protein Rab-23/0.516
1lfdGNPGTPase HRas/0.515
4ldjGDPGTPase KRas/0.515
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.511
2msdGNPMHC class I alpha chain/0.510
2fg5GNPRas-related protein Rab-31/0.509
3th5GNPRas-related C3 botulinum toxin substrate 1/0.508
2mscGDPMHC class I alpha chain/0.507
4js0GNPCell division control protein 42 homolog/0.506
4ol0GTPGTP-binding nuclear protein Ran/0.506
1gwnGTPRho-related GTP-binding protein RhoE/0.504
1d5cGDPGTPase (Rab6)/0.503
3kz1GSPTransforming protein RhoA/0.503
1yu9GNPRas-related protein Rab-4A/0.501
1z2cGNPRho-related GTP-binding protein RhoC/0.497
2bmeGNPRas-related protein Rab-4A/0.495
1xtsGTPGTP-binding protein Rheb/0.491
2cl6CAGGTPase HRas/0.491
1ow3GDPTransforming protein RhoA/0.488
4dxaGSPRas-related protein Rap-1b/0.487
1ibrGNPGTP-binding nuclear protein Ran/0.485
3tklGTPRas-related protein Rab-1A/0.484
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.480
4uj3GNPRas-related protein Rab-11A/0.477
4cidANPEH domain-containing protein 2/0.476
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.475
3nbzGTPGTP-binding nuclear protein Ran/0.475
4o2rGDPGTP-binding protein Rheb/0.474
1g16GDPRas-related protein SEC4/0.471
3c14FOKAdenylate cyclase type 2/0.470
3c14FOKAdenylate cyclase type 5/0.470
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.469
3eg5GNPCell division control protein 42 homolog/0.468
4edz0O5Hematopoietic prostaglandin D synthase/0.467
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.466
3cphGDPRas-related protein SEC4/0.465
3ddw055Glycogen phosphorylase, liver form2.4.1.10.459
2r6jNDPEugenol synthase 11.1.1.3180.458
4nhyPD2Prolyl 3-hydroxylase OGFOD11.14.110.458
1uadGNPRas-related protein Ral-A/0.457
4n3l2FNProthrombin3.4.21.50.457
2xvw9NRSerum albumin/0.456
4pkwGM6Lethal factor3.4.24.830.456
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.455
2xvv9DNSerum albumin/0.454
1rzuADPGlycogen synthase 12.4.1.210.453
3a783EVVitamin D3 receptor/0.452
3iogSDFMetallo-beta-lactamase type 2/0.452
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.452
2p1v5TNRetinoic acid receptor RXR-alpha/0.451
2a9y26AAdenosine kinase2.7.1.200.450
1ve3SAMUncharacterized protein/0.449
2h15B19Carbonic anhydrase 24.2.1.10.448
4iteTEYVitamin D3 receptor/0.448
2lbvEB4Extracellular fatty acid-binding protein/0.447
4bamMM9Prothrombin3.4.21.50.447
2bfmTOPPteridine reductase 11.5.1.330.446
3kxoKXOHematopoietic prostaglandin D synthase/0.446
3mjhGTPRas-related protein Rab-5A/0.446
3tl1JROPutative polyketide cyclase/0.446
3vhxGTPADP-ribosylation factor 6/0.446
4fhd0TTSpore photoproduct lyase/0.446
2vczVC3Hematopoietic prostaglandin D synthase/0.445
5iqgGDPBifunctional AAC/APH2.3.10.445
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
3b9lAZZSerum albumin/0.444
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.444
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.443
2zsiGA4Gibberellin receptor GID1A30.443
3djfBC3Purine nucleoside phosphorylase/0.443
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.443
4g0k0VSGlutathionyl-hydroquinone reductase YqjG1.80.443
4rtbSAMPutative thiazole biosynthesis protein ThiH/0.443
2bxqIMNSerum albumin/0.442
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.442
4gusFADLysine-specific histone demethylase 1B10.442
5dstSAHProtein arginine N-methyltransferase 82.1.10.442
5hpyGDPTransforming protein RhoA/0.442
5iubCLRAdenosine receptor A2a/0.442
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.441
1kceCB3Thymidylate synthase/0.441
1n5tOALActVA 6 protein/0.441
3fhxPXLPyridoxal kinase2.7.1.350.441
4knmE1ECarbonic anhydrase 134.2.1.10.441
5c46GSPRas-related protein Rab-11A/0.441
5kf2COAPredicted acetyltransferase/0.441
1crbRTLRetinol-binding protein 1/0.440
1kmyBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.440
1ygjRMCPyridoxal kinase2.7.1.350.440
3dr1C5DVitamin D3 receptor A/0.440
4g2i0VQVitamin D3 receptor/0.440
4q0a4OAVitamin D3 receptor A/0.440
4uhrNGIAdenosine receptor A2a/0.440