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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
4dlzGNPGTPase HRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4dlzGNPGTPase HRas/1.000
4dlxGNPGTPase HRas/0.882
2rgcGNPGTPase HRas/0.873
2rgbGNPGTPase HRas/0.836
4dlvGNPGTPase HRas/0.823
3rs0GNPGTPase HRas/0.798
3rs5GNPGTPase HRas/0.798
3rs7GNPGTPase HRas/0.798
2rgeGNPGTPase HRas/0.797
3rslGNPGTPase HRas/0.787
3oivGNPGTPase HRas/0.778
3lbnGNPGTPase HRas/0.748
4dlwGNPGTPase HRas/0.722
3v4fGNPGTPase HRas/0.713
4dlsGNPGTPase HRas/0.711
3l8yGNPGTPase HRas/0.683
4l9wGNPGTPase HRas/0.663
4nyiGNPGTPase HRas/0.662
3k8yGNPGTPase HRas/0.661
4g0nGNPGTPase HRas/0.653
3ddcGNPGTPase HRas/0.648
2c5lGTPGTPase HRas/0.644
3x1zGNPRas-related protein Rap-1b/0.641
3rs4GNPGTPase HRas/0.640
5b2zGNPGTPase HRas/0.639
3oiuGNPGTPase HRas/0.632
5difGNPGTP-binding nuclear protein Ran/0.631
4dsnGCPGTPase KRas/0.628
1e96GTPRas-related C3 botulinum toxin substrate 1/0.627
3i3sGNPGTPase HRas/0.624
3oiwGNPGTPase HRas/0.623
3kkoGNPRas-related protein M-Ras/0.622
3a6pGTPGTP-binding nuclear protein Ran/0.618
4hdoGNPRas-related protein Rap-1b/0.618
1g17GNPRas-related protein SEC4/0.617
4k81GTPGTPase HRas/0.614
3kucGDPRas-related protein Rap-1A/0.612
3pitGNPRas-related protein M-Ras/0.612
4nyjGNPGTPase HRas/0.609
3oesGNPGTPase RhebL1/0.606
3w3zGTPGTP-binding nuclear protein Ran/0.606
1t91GTPRas-related protein Rab-7a/0.603
4rkfGNPRas-related protein Rab-3/0.602
4l9sGDPGTPase HRas/0.593
4lhwGNPRas-related protein Rab-8A/0.593
3e5hGNPRas-related protein Rab-28/0.591
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.590
1zd9GDPADP-ribosylation factor-like protein 8A/0.587
3kudGDPGTPase HRas/0.587
1xtsGTPGTP-binding protein Rheb/0.586
5jljGNPGTP-binding nuclear protein Ran/0.586
3lbiGNPGTPase HRas/0.585
3rabGNPRas-related protein Rab-3A/0.583
3ea5GDPGTP-binding nuclear protein Ran/0.581
4ol0GTPGTP-binding nuclear protein Ran/0.575
1ibrGNPGTP-binding nuclear protein Ran/0.574
4mitGTPRho-related protein racC/0.573
3lbhGNPGTPase HRas/0.572
4hdqGNPRas-related protein Rap-1b/0.572
5dhaGNPGTP-binding nuclear protein Ran/0.569
2bkuGTPGTP-binding nuclear protein Ran/0.568
4dltGNPGTPase HRas/0.568
1xtrGNPGTP-binding protein Rheb/0.565
3a58GNPGTP-binding protein RHO1/0.565
4tq9GDPGTPase KRas/0.562
1m7bGTPRho-related GTP-binding protein RhoE/0.561
2fe4GDPRas-related protein Rab-6B/0.560
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.560
1yzqGNPRas-related protein Rab-6A/0.559
1zbdGTPRas-related protein Rab-3A/0.555
3bbpGTPRas-related protein Rab-6A/0.555
4lv6GDPGTPase KRas/0.555
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.554
4l8gGDPGTPase KRas/0.554
2zetGTPRas-related protein Rab-27B/0.552
1zc3GNPRas-related protein Ral-A/0.550
4qxaGTPRas-related protein Rab-9A/0.548
4dsoGSPGTPase KRas/0.547
4kvgGTPRas-related protein Rap-1A/0.547
3nbzGTPGTP-binding nuclear protein Ran/0.546
1zc4GNPRas-related protein Ral-A/0.545
3tsoGNPRas-related protein Rab-25/0.545
1a2bGSPTransforming protein RhoA/0.544
3kkqGDPRas-related protein M-Ras/0.544
3th5GNPRas-related C3 botulinum toxin substrate 1/0.544
2gcpGSPRho-related GTP-binding protein RhoC/0.542
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.541
1kmqGNPTransforming protein RhoA/0.540
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.540
2msdGNPMHC class I alpha chain/0.539
4obeGDPGTPase KRas/0.538
1cxzGSPTransforming protein RhoA/0.537
4dxaGSPRas-related protein Rap-1b/0.537
2gilGTPRas-related protein Rab-6A/0.536
1vg8GNPRas-related protein Rab-7a/0.535
3tgpGNPGTPase HRas/0.534
1x1rGDPRas-related protein M-Ras/0.531
4ql3GDPGTPase KRas/0.529
2ce2GDPGTPase HRas/0.528
1oixGDPRas-related protein Rab-11A/0.527
3wyfGTPGTP-binding nuclear protein/0.527
3tnfGNPRas-related protein Rab-8A/0.526
4epwGDPGTPase KRas/0.525
4epxGDPGTPase KRas/0.525
4o25GTPGTP-binding protein Rheb/0.525
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.523
4xvrGNPGTPase HRas/0.523
4q02GDPGTPase KRas/0.522
1lfdGNPGTPase HRas/0.521
4wa7GDPGTPase KRas/0.521
4lpkGDPGTPase KRas/0.520
2ffqGSPRas-related protein Rab-6B/0.519
1k5dGNPGTP-binding nuclear protein Ran/0.518
1s1cGNPTransforming protein RhoA/0.518
4lucGDPGTPase KRas/0.518
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.517
3lawGNPRas-related protein Rab-7a/0.516
1gwnGTPRho-related GTP-binding protein RhoE/0.515
3bc1GNPRas-related protein Rab-27A/0.515
4lrwGDPGTPase KRas/0.515
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.514
3cphGDPRas-related protein SEC4/0.512
4ldjGDPGTPase KRas/0.511
1z0dGDPRas-related protein Rab-5C/0.508
4uj3GNPRas-related protein Rab-11A/0.508
4xvqGNPGTPase HRas/0.507
3k9lGNPGTPase HRas/0.506
4o2lGTPGTP-binding protein Rheb/0.504
1d5cGDPGTPase (Rab6)/0.503
1ow3GDPTransforming protein RhoA/0.503
2mscGDPMHC class I alpha chain/0.503
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.503
3kz1GSPTransforming protein RhoA/0.503
3x1wGDPRas-related protein Rap-1b/0.503
2rggGNPGTPase HRas/0.501
4js0GNPCell division control protein 42 homolog/0.501
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.499
4o2rGDPGTP-binding protein Rheb/0.499
1z2aGDPRas-related protein Rab-23/0.497
1uadGNPRas-related protein Ral-A/0.495
2fg5GNPRas-related protein Rab-31/0.495
4q03GDPGTPase KRas/0.495
1yu9GNPRas-related protein Rab-4A/0.494
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.492
3mjhGTPRas-related protein Rab-5A/0.491
4cymGCPRas-related protein Rab-32/0.491
4cidANPEH domain-containing protein 2/0.490
4dsuGDPGTPase KRas/0.488
1g16GDPRas-related protein SEC4/0.486
3tklGTPRas-related protein Rab-1A/0.486
1tu3GNPRas-related protein Rab-5A/0.484
3eg5GNPCell division control protein 42 homolog/0.480
2gvdFKPAdenylate cyclase type 2/0.479
2gvdFKPAdenylate cyclase type 5/0.479
3qbtGNPRas-related protein Rab-8A/0.479
2bmeGNPRas-related protein Rab-4A/0.478
4xoiGTPTransforming protein RhoA/0.478
1z0aGDPRas-related protein Rab-2A/0.476
5hpyGDPTransforming protein RhoA/0.475
4uj5GNPRas-related protein Rab-11A/0.474
1z2cGNPRho-related GTP-binding protein RhoC/0.472
2cl6CAGGTPase HRas/0.472
2mseGNPMHC class I alpha chain/0.471
3c14FOKAdenylate cyclase type 2/0.470
3c14FOKAdenylate cyclase type 5/0.470
5c46GSPRas-related protein Rab-11A/0.470
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.469
3w0aDS5Vitamin D3 receptor/0.460
2bf7HBIPteridine reductase 11.5.1.330.458
1crbRTLRetinol-binding protein 1/0.456
2hamC33Vitamin D3 receptor/0.456
3t1tGDPProbable gliding protein mglA/0.456
1n6lGTPRas-related protein Rab-5A/0.454
4q0a4OAVitamin D3 receptor A/0.454
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.453
4xg1LLPDiaminopimelate decarboxylase/0.453
3f0aACOSpermidine N(1)-acetyltransferase/0.452
1v8kANPKinesin-like protein KIF2C/0.450
1ie9VDXVitamin D3 receptor/0.449
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.449
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.449
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.448
1db1VDXVitamin D3 receptor/0.447
1cjtFOKAdenylate cyclase type 2/0.446
1cjtFOKAdenylate cyclase type 5/0.446
1krv147Galactoside O-acetyltransferase2.3.1.180.446
4edz0O5Hematopoietic prostaglandin D synthase/0.446
2vczVC3Hematopoietic prostaglandin D synthase/0.445
1kphSAHCyclopropane mycolic acid synthase 12.1.1.790.444
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.444
3iktNADRedox-sensing transcriptional repressor Rex/0.444
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
1n83CLRNuclear receptor ROR-alpha/0.443
2vcwZZAHematopoietic prostaglandin D synthase/0.443
4ihjGTPTubulin alpha-1B chain/0.443
4iteTEYVitamin D3 receptor/0.443
4qzuRTLRetinol-binding protein 2/0.442
5k2dZMAAdenosine receptor A2a/0.442
1cjuFOKAdenylate cyclase type 2/0.441
1cjuFOKAdenylate cyclase type 5/0.441
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
5h8tRTLRetinol-binding protein 1/0.441
1mrqSTRAldo-keto reductase family 1 member C1/0.440
2bfaCB3Pteridine reductase 11.5.1.330.440
2vcqD25Hematopoietic prostaglandin D synthase/0.440
4bfrJ82Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform2.7.1.1530.440
4ead0NPThymidine phosphorylase2.4.2.40.440
4jdaA9SAbscisic acid receptor PYL3/0.440