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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
3kudGDPGTPase HRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3kudGDPGTPase HRas/1.000
3oiwGNPGTPase HRas/0.699
4nyiGNPGTPase HRas/0.637
3w3zGTPGTP-binding nuclear protein Ran/0.630
3oiuGNPGTPase HRas/0.623
3l8yGNPGTPase HRas/0.617
3nbzGTPGTP-binding nuclear protein Ran/0.617
3rslGNPGTPase HRas/0.617
4dltGNPGTPase HRas/0.617
2c5lGTPGTPase HRas/0.616
3kkoGNPRas-related protein M-Ras/0.616
4nyjGNPGTPase HRas/0.614
3ddcGNPGTPase HRas/0.610
4dlwGNPGTPase HRas/0.610
2rgbGNPGTPase HRas/0.609
5dhaGNPGTP-binding nuclear protein Ran/0.609
3lbnGNPGTPase HRas/0.606
3v4fGNPGTPase HRas/0.603
5b2zGNPGTPase HRas/0.603
1ibrGNPGTP-binding nuclear protein Ran/0.601
2bkuGTPGTP-binding nuclear protein Ran/0.600
3rs5GNPGTPase HRas/0.600
3rs7GNPGTPase HRas/0.600
4dsnGCPGTPase KRas/0.600
5difGNPGTP-binding nuclear protein Ran/0.599
3ea5GDPGTP-binding nuclear protein Ran/0.598
3i3sGNPGTPase HRas/0.596
3rs0GNPGTPase HRas/0.596
3pitGNPRas-related protein M-Ras/0.594
1k5dGNPGTP-binding nuclear protein Ran/0.592
3rs4GNPGTPase HRas/0.591
1t91GTPRas-related protein Rab-7a/0.590
1xtsGTPGTP-binding protein Rheb/0.590
3a6pGTPGTP-binding nuclear protein Ran/0.590
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.590
4hdoGNPRas-related protein Rap-1b/0.590
1e96GTPRas-related C3 botulinum toxin substrate 1/0.589
5jljGNPGTP-binding nuclear protein Ran/0.587
1g17GNPRas-related protein SEC4/0.586
4dlxGNPGTPase HRas/0.585
4dlzGNPGTPase HRas/0.585
1vg8GNPRas-related protein Rab-7a/0.584
1xtrGNPGTP-binding protein Rheb/0.583
3oivGNPGTPase HRas/0.583
4dlvGNPGTPase HRas/0.583
1zbdGTPRas-related protein Rab-3A/0.582
3oesGNPGTPase RhebL1/0.582
4g0nGNPGTPase HRas/0.581
4mitGTPRho-related protein racC/0.581
3tsoGNPRas-related protein Rab-25/0.580
2rgcGNPGTPase HRas/0.579
3e5hGNPRas-related protein Rab-28/0.579
3bbpGTPRas-related protein Rab-6A/0.578
4l9wGNPGTPase HRas/0.578
4lhwGNPRas-related protein Rab-8A/0.576
3kucGDPRas-related protein Rap-1A/0.575
4o25GTPGTP-binding protein Rheb/0.575
1yzqGNPRas-related protein Rab-6A/0.574
2gilGTPRas-related protein Rab-6A/0.574
3lbhGNPGTPase HRas/0.574
4dsoGSPGTPase KRas/0.574
4epwGDPGTPase KRas/0.574
1yhnGTPRas-related protein Rab-7a/0.573
4k81GTPGTPase HRas/0.573
4dlsGNPGTPase HRas/0.572
1zd9GDPADP-ribosylation factor-like protein 8A/0.571
4rkfGNPRas-related protein Rab-3/0.571
3x1zGNPRas-related protein Rap-1b/0.570
1zc4GNPRas-related protein Ral-A/0.569
1zc3GNPRas-related protein Ral-A/0.566
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.564
2zetGTPRas-related protein Rab-27B/0.562
3lbiGNPGTPase HRas/0.562
2rgeGNPGTPase HRas/0.561
2fe4GDPRas-related protein Rab-6B/0.559
3wyfGTPGTP-binding nuclear protein/0.557
1cxzGSPTransforming protein RhoA/0.556
3rabGNPRas-related protein Rab-3A/0.553
4kvgGTPRas-related protein Rap-1A/0.553
4l9sGDPGTPase HRas/0.553
4tq9GDPGTPase KRas/0.551
4o2rGDPGTP-binding protein Rheb/0.550
1kmqGNPTransforming protein RhoA/0.546
2ffqGSPRas-related protein Rab-6B/0.546
3kz1GSPTransforming protein RhoA/0.545
4q03GDPGTPase KRas/0.544
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.543
3k8yGNPGTPase HRas/0.543
4qxaGTPRas-related protein Rab-9A/0.543
1s1cGNPTransforming protein RhoA/0.542
4hdqGNPRas-related protein Rap-1b/0.542
1a2bGSPTransforming protein RhoA/0.540
4epxGDPGTPase KRas/0.540
4ql3GDPGTPase KRas/0.539
1ow3GDPTransforming protein RhoA/0.538
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.538
4lucGDPGTPase KRas/0.536
4ol0GTPGTP-binding nuclear protein Ran/0.535
4xvrGNPGTPase HRas/0.535
1m7bGTPRho-related GTP-binding protein RhoE/0.534
1z2aGDPRas-related protein Rab-23/0.533
3a58GNPGTP-binding protein RHO1/0.533
3cphGDPRas-related protein SEC4/0.532
3th5GNPRas-related C3 botulinum toxin substrate 1/0.532
3x1wGDPRas-related protein Rap-1b/0.532
4dxaGSPRas-related protein Rap-1b/0.532
4xvqGNPGTPase HRas/0.532
2gcpGSPRho-related GTP-binding protein RhoC/0.531
4uj3GNPRas-related protein Rab-11A/0.531
3kkqGDPRas-related protein M-Ras/0.529
3lawGNPRas-related protein Rab-7a/0.529
4l8gGDPGTPase KRas/0.528
4wa7GDPGTPase KRas/0.528
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.527
3tnfGNPRas-related protein Rab-8A/0.527
1oixGDPRas-related protein Rab-11A/0.526
4obeGDPGTPase KRas/0.526
1x1rGDPRas-related protein M-Ras/0.525
3bc1GNPRas-related protein Rab-27A/0.525
1d5cGDPGTPase (Rab6)/0.524
2msdGNPMHC class I alpha chain/0.524
1z2cGNPRho-related GTP-binding protein RhoC/0.523
2rggGNPGTPase HRas/0.522
3tgpGNPGTPase HRas/0.522
2clsGTPRho-related GTP-binding protein Rho6/0.520
4dsuGDPGTPase KRas/0.520
1g16GDPRas-related protein SEC4/0.519
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.518
4xoiGTPTransforming protein RhoA/0.517
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.516
4lpkGDPGTPase KRas/0.516
4lv6GDPGTPase KRas/0.516
4o2lGTPGTP-binding protein Rheb/0.516
3eg5GNPCell division control protein 42 homolog/0.515
4cidANPEH domain-containing protein 2/0.515
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.515
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.513
2ce2GDPGTPase HRas/0.511
2cl6CAGGTPase HRas/0.511
3qbtGNPRas-related protein Rab-8A/0.510
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.509
4q02GDPGTPase KRas/0.506
4ldjGDPGTPase KRas/0.505
5hpyGDPTransforming protein RhoA/0.505
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.499
4cymGCPRas-related protein Rab-32/0.499
2w71L23Biotin carboxylase6.3.4.140.496
3mjhGTPRas-related protein Rab-5A/0.491
1z0aGDPRas-related protein Rab-2A/0.487
1uadGNPRas-related protein Ral-A/0.482
1gwnGTPRho-related GTP-binding protein RhoE/0.481
1z0dGDPRas-related protein Rab-5C/0.479
1n6lGTPRas-related protein Rab-5A/0.476
3akm11DFatty acid-binding protein, intestinal/0.476
1lfdGNPGTPase HRas/0.475
4js0GNPCell division control protein 42 homolog/0.474
3k9lGNPGTPase HRas/0.472
2fg5GNPRas-related protein Rab-31/0.471
4lrwGDPGTPase KRas/0.471
3sfxJANUncharacterized protein/0.470
4lb2DM5Serum albumin/0.470
4mv1ADPBiotin carboxylase6.3.4.140.470
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.469
3t1tGDPProbable gliding protein mglA/0.467
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.467
4ead0NPThymidine phosphorylase2.4.2.40.467
2mseGNPMHC class I alpha chain/0.466
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.466
4uj5GNPRas-related protein Rab-11A/0.466
1n83CLRNuclear receptor ROR-alpha/0.465
3x04GNPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.465
3zeiAWHO-acetylserine sulfhydrylase/0.465
2rds1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.464
3tklGTPRas-related protein Rab-1A/0.464
5iu4ZMAAdenosine receptor A2a/0.464
2mscGDPMHC class I alpha chain/0.461
2bmeGNPRas-related protein Rab-4A/0.460
3x065GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.460
3tfyCOAN-alpha-acetyltransferase 502.3.10.459
1p8dCO1Oxysterols receptor LXR-beta/0.458
3p67FMNPentaerythritol tetranitrate reductase/0.458
3pqbVGPPutative oxidoreductase/0.458
1tu3GNPRas-related protein Rab-5A/0.456
4b2gV1NUncharacterized protein/0.456
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.456
3c14FOKAdenylate cyclase type 2/0.455
3c14FOKAdenylate cyclase type 5/0.455
3oqkS52Renin3.4.23.150.455
5iubCLRAdenosine receptor A2a/0.455
2zsaADPPantothenate kinase2.7.1.330.454
2e0nSAHPrecorrin-2 C20-methyltransferase/0.453
4ffrATPUncharacterized protein/0.453
3adaNADSubunit alpha of sarocosine oxidase/0.450
4ycoFMNtRNA-dihydrouridine(16) synthase/0.450
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.449
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.449
5c46GSPRas-related protein Rab-11A/0.449
3emlZMAAdenosine receptor A2a/0.449
1t13INI6,7-dimethyl-8-ribityllumazine synthase 2/0.447
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.447
1n5tOALActVA 6 protein/0.446
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.446
2xvfFADPutative flavin-containing monooxygenase/0.446
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.446
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.446
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.445
2gvdFKPAdenylate cyclase type 2/0.445
2gvdFKPAdenylate cyclase type 5/0.445
3nr4PYVAbscisic acid receptor PYL2/0.445
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.445
1l2oADPMyosin heavy chain, striated muscle/0.444
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.444
1txiTX5Vitamin D3 receptor/0.444
2v59LZKBiotin carboxylase6.3.4.140.444
2z4sADPChromosomal replication initiator protein DnaA/0.444
3dgeADPSensor histidine kinase/0.444
4b4dFADFerredoxin-NADP reductase/0.444
4eiyZMAAdenosine receptor A2a/0.444
4lutDCSAlanine racemase/0.444
1rzuADPGlycogen synthase 12.4.1.210.443
3c3xNAPEugenol synthase 11.1.1.3180.443
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.443
4tx9AMZPhosphoribosyl isomerase A/0.443
1jnzFADAdenylylsulfate reductase, subunit A (AprA)/0.442
2z9dFMNFMN-dependent NADH-azoreductase/0.442
4lzwTHMUridine phosphorylase/0.442
4m2bUPGUDP-glucose pyrophosphorylase/0.442
1eiiRTLRetinol-binding protein 2/0.441
1fmjRTLRetinol dehydratase/0.441
2c2aADPSensor histidine kinase/0.441
2qx7NAPEugenol synthase 11.1.1.3180.441
3jzdNADMaleylacetate reductase/0.441
4ixd1HVIntegrin alpha-L/0.441
1nhz486Glucocorticoid receptor/0.440
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.440
2hamC33Vitamin D3 receptor/0.440
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
3ix4TX1Transcriptional activator protein LasR/0.440
3kroIPEGeranyl diphosphate synthase large subunit/0.440
3vf60H6Glucokinase2.7.1.20.440
3w0aDS5Vitamin D3 receptor/0.440