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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
3x1zGNPRas-related protein Rap-1b

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3x1zGNPRas-related protein Rap-1b/1.000
3pitGNPRas-related protein M-Ras/0.650
3v4fGNPGTPase HRas/0.644
4dsnGCPGTPase KRas/0.643
3lbnGNPGTPase HRas/0.638
2rgcGNPGTPase HRas/0.637
3rs0GNPGTPase HRas/0.637
3ddcGNPGTPase HRas/0.633
4dlzGNPGTPase HRas/0.631
4dlxGNPGTPase HRas/0.629
3k8yGNPGTPase HRas/0.628
2rgeGNPGTPase HRas/0.627
5b2zGNPGTPase HRas/0.621
3kkoGNPRas-related protein M-Ras/0.620
2rgbGNPGTPase HRas/0.609
3i3sGNPGTPase HRas/0.607
4dlwGNPGTPase HRas/0.604
3oiwGNPGTPase HRas/0.601
3rs5GNPGTPase HRas/0.601
2c5lGTPGTPase HRas/0.599
3oivGNPGTPase HRas/0.599
4g0nGNPGTPase HRas/0.597
3l8yGNPGTPase HRas/0.596
3lbhGNPGTPase HRas/0.595
4dltGNPGTPase HRas/0.595
3rslGNPGTPase HRas/0.593
3e5hGNPRas-related protein Rab-28/0.590
4dlvGNPGTPase HRas/0.590
4nyiGNPGTPase HRas/0.590
1t91GTPRas-related protein Rab-7a/0.585
3kucGDPRas-related protein Rap-1A/0.584
3a6pGTPGTP-binding nuclear protein Ran/0.581
3rs7GNPGTPase HRas/0.581
4rkfGNPRas-related protein Rab-3/0.578
3rs4GNPGTPase HRas/0.577
5jljGNPGTP-binding nuclear protein Ran/0.575
3bbpGTPRas-related protein Rab-6A/0.574
3oiuGNPGTPase HRas/0.572
4hdoGNPRas-related protein Rap-1b/0.571
4dlsGNPGTPase HRas/0.568
4nyjGNPGTPase HRas/0.568
4tq9GDPGTPase KRas/0.568
5difGNPGTP-binding nuclear protein Ran/0.568
3ea5GDPGTP-binding nuclear protein Ran/0.566
1zd9GDPADP-ribosylation factor-like protein 8A/0.565
4qxaGTPRas-related protein Rab-9A/0.564
2bkuGTPGTP-binding nuclear protein Ran/0.562
3oesGNPGTPase RhebL1/0.560
3lbiGNPGTPase HRas/0.556
1d5cGDPGTPase (Rab6)/0.554
1e96GTPRas-related C3 botulinum toxin substrate 1/0.553
1zbdGTPRas-related protein Rab-3A/0.553
4mitGTPRho-related protein racC/0.552
3wyfGTPGTP-binding nuclear protein/0.551
3nbzGTPGTP-binding nuclear protein Ran/0.550
1yzqGNPRas-related protein Rab-6A/0.549
3w3zGTPGTP-binding nuclear protein Ran/0.546
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.544
2fe4GDPRas-related protein Rab-6B/0.543
1ibrGNPGTP-binding nuclear protein Ran/0.542
4l9wGNPGTPase HRas/0.540
5dhaGNPGTP-binding nuclear protein Ran/0.535
3kudGDPGTPase HRas/0.534
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.534
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.532
4obeGDPGTPase KRas/0.531
3rabGNPRas-related protein Rab-3A/0.530
4hdqGNPRas-related protein Rap-1b/0.527
3kkqGDPRas-related protein M-Ras/0.526
4epxGDPGTPase KRas/0.526
1kmqGNPTransforming protein RhoA/0.525
1yhnGTPRas-related protein Rab-7a/0.525
4kvgGTPRas-related protein Rap-1A/0.523
4q03GDPGTPase KRas/0.522
1x1rGDPRas-related protein M-Ras/0.521
1g17GNPRas-related protein SEC4/0.520
3cphGDPRas-related protein SEC4/0.518
1xtsGTPGTP-binding protein Rheb/0.517
4ql3GDPGTPase KRas/0.515
1oixGDPRas-related protein Rab-11A/0.513
1lfdGNPGTPase HRas/0.511
3tgpGNPGTPase HRas/0.511
4epwGDPGTPase KRas/0.511
3tsoGNPRas-related protein Rab-25/0.510
1k5dGNPGTP-binding nuclear protein Ran/0.507
2msdGNPMHC class I alpha chain/0.507
4ldjGDPGTPase KRas/0.506
4o25GTPGTP-binding protein Rheb/0.506
3a58GNPGTP-binding protein RHO1/0.505
4l9sGDPGTPase HRas/0.505
2ce2GDPGTPase HRas/0.504
1yu9GNPRas-related protein Rab-4A/0.503
2fg5GNPRas-related protein Rab-31/0.500
2zetGTPRas-related protein Rab-27B/0.500
1xtrGNPGTP-binding protein Rheb/0.499
3th5GNPRas-related C3 botulinum toxin substrate 1/0.499
4cidANPEH domain-containing protein 2/0.499
4xvrGNPGTPase HRas/0.499
1vg8GNPRas-related protein Rab-7a/0.495
2rggGNPGTPase HRas/0.494
4lpkGDPGTPase KRas/0.494
5hpyGDPTransforming protein RhoA/0.494
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.493
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.493
2ffqGSPRas-related protein Rab-6B/0.492
4o2rGDPGTP-binding protein Rheb/0.492
4dsoGSPGTPase KRas/0.491
4o2lGTPGTP-binding protein Rheb/0.491
4lv6GDPGTPase KRas/0.490
3fhxPLPPyridoxal kinase2.7.1.350.489
1gwnGTPRho-related GTP-binding protein RhoE/0.488
4wa7GDPGTPase KRas/0.488
2gcpGSPRho-related GTP-binding protein RhoC/0.487
4xoiGTPTransforming protein RhoA/0.487
1z2aGDPRas-related protein Rab-23/0.486
1s1cGNPTransforming protein RhoA/0.484
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.484
3w0aDS5Vitamin D3 receptor/0.484
4xvqGNPGTPase HRas/0.484
1a2bGSPTransforming protein RhoA/0.483
1db1VDXVitamin D3 receptor/0.483
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.483
1crbRTLRetinol-binding protein 1/0.482
1n6lGTPRas-related protein Rab-5A/0.482
4l8gGDPGTPase KRas/0.481
4uj3GNPRas-related protein Rab-11A/0.481
4q02GDPGTPase KRas/0.479
4iteTEYVitamin D3 receptor/0.478
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.477
2hamC33Vitamin D3 receptor/0.476
3qbtGNPRas-related protein Rab-8A/0.476
4qzuRTLRetinol-binding protein 2/0.476
1cxzGSPTransforming protein RhoA/0.472
3a783EVVitamin D3 receptor/0.472
3k7mFAD6-hydroxy-L-nicotine oxidase/0.472
4itfTFYVitamin D3 receptor/0.472
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.471
2zlcVDXVitamin D3 receptor/0.471
1s19MC9Vitamin D3 receptor/0.470
2bmeGNPRas-related protein Rab-4A/0.470
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.469
1txiTX5Vitamin D3 receptor/0.468
2gvdFKPAdenylate cyclase type 2/0.468
2gvdFKPAdenylate cyclase type 5/0.468
3k9lGNPGTPase HRas/0.468
3p74FMNPentaerythritol tetranitrate reductase/0.467
3x1wGDPRas-related protein Rap-1b/0.467
4js0GNPCell division control protein 42 homolog/0.466
5k2cZMAAdenosine receptor A2a/0.466
5iu4ZMAAdenosine receptor A2a/0.465
3zvuA8SAbscisic acid receptor PYR1/0.464
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.464
3gl2D3MDdmC/0.463
2mscGDPMHC class I alpha chain/0.462
1ysiN3BBcl-2-like protein 1/0.461
3gyaCOAGCN5-related N-acetyltransferase/0.461
1g16GDPRas-related protein SEC4/0.460
3kz1GSPTransforming protein RhoA/0.460
3w0hW12Vitamin D3 receptor/0.460
5jtbZMAAdenosine receptor A2a/0.460
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.459
3w0yDS4Vitamin D3 receptor/0.459
4g2i0VQVitamin D3 receptor/0.459
2yg4FADPutrescine oxidase/0.458
3dr1C5DVitamin D3 receptor A/0.458
1rd4L08Integrin alpha-L/0.457
2j9lATPH(+)/Cl(-) exchange transporter 5/0.457
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.456
2harOCCVitamin D3 receptor/0.456
3gbuATPUncharacterized sugar kinase PH14592.7.10.456
5iu86DZAdenosine receptor A2a/0.456
5k2dZMAAdenosine receptor A2a/0.456
1towCRZFatty acid-binding protein, adipocyte/0.455
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
4bfwZVWPantothenate kinase2.7.1.330.455
4du82P0Mevalonate diphosphate decarboxylase/0.454
4f700STCyclin-dependent kinase 82.7.11.220.454
2hb8MVDVitamin D3 receptor/0.453
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.453
3m7rVDXVitamin D3 receptor/0.453
3t1tGDPProbable gliding protein mglA/0.453
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.453
5hbsRTLRetinol-binding protein 1/0.453
5iubCLRAdenosine receptor A2a/0.453
3w0c6DSVitamin D3 receptor/0.452
2hc4VDXVitamin D3 receptor A/0.451
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.450
2ok7FADFerredoxin--NADP reductase, apicoplast/0.450
3pqbVGPPutative oxidoreductase/0.450
3sfh1DIHistone deacetylase 83.5.1.980.450
3vg9ZMAAdenosine receptor A2a/0.450
1dr3TAPDihydrofolate reductase1.5.1.30.449
1s3uTQDDihydrofolate reductase1.5.1.30.449
2xvv9DNSerum albumin/0.449
3bc1GNPRas-related protein Rab-27A/0.449
5h8tRTLRetinol-binding protein 1/0.449
2r6jNDPEugenol synthase 11.1.1.3180.448
3h4vDVPPteridine reductase 11.5.1.330.448
3vt3VDXVitamin D3 receptor/0.448
3vtcTK3Vitamin D3 receptor/0.448
3up0D7SaceDAF-12/0.447
4cavMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.447
2z4sADPChromosomal replication initiator protein DnaA/0.446
4la7A1OAbscisic acid receptor PYL2/0.446
5esoTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.446
1sze173Cytochrome b2, mitochondrial1.1.2.30.445
4ead0NPThymidine phosphorylase2.4.2.40.445
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.444
2hb7O1CVitamin D3 receptor/0.444
2hbhXE4Vitamin D3 receptor A/0.444
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.444
4cymGCPRas-related protein Rab-32/0.444
4u9vACON-alpha-acetyltransferase 402.3.10.444
2a9z26AAdenosine kinase2.7.1.200.443
2o4rVD5Vitamin D3 receptor/0.443
4g2h0VQVitamin D3 receptor A/0.443
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.442
2j5xGSPADP-ribosylation factor 6/0.442
2wueKEK4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.442
3bgxMEFThymidylate synthase/0.442
3cobADPKinesin heavy chain-like protein/0.442
3nn6HNK6-hydroxy-L-nicotine oxidase/0.442
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.442
1rk3VDXVitamin D3 receptor/0.441
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2bfaCB3Pteridine reductase 11.5.1.330.441
3gb4D3MDdmC/0.441
3vf60H6Glucokinase2.7.1.20.441
3w0jT08Vitamin D3 receptor/0.441
4ys0ADPProtein translocase subunit SecA/0.441
5k2bZMAAdenosine receptor A2a/0.441
1mvsDTMDihydrofolate reductase1.5.1.30.440
1n71COAAac(6')-Ii protein/0.440
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.440
5kf1COAPredicted acetyltransferase/0.440