Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3tc53T5Peptidyl-prolyl cis-trans isomerase NIMA-interacting 15.2.1.8

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3tc53T5Peptidyl-prolyl cis-trans isomerase NIMA-interacting 15.2.1.81.000
3dds26BGlycogen phosphorylase, liver form2.4.1.10.514
3wsjMK1Protease/0.499
3kai4FIPeptidyl-prolyl cis-trans isomerase NIMA-interacting 15.2.1.80.497
2oo7AP5Adenylate kinase/0.493
2harOCCVitamin D3 receptor/0.491
4g95OAGDihydrofolate reductase1.5.1.30.488
1wuuANPGalactokinase2.7.1.60.486
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.485
1m8jNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.484
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.482
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.482
4jq2SUZAldo-keto reductase family 1 member C2/0.480
1upw444Oxysterols receptor LXR-beta/0.479
2g86UMPThymidylate synthase/0.479
1kqwRTLCellular retinol-binding protein type II/0.478
1blzACVIsopenicillin N synthase1.21.3.10.477
2hc4VDXVitamin D3 receptor A/0.477
3w5rLOAVitamin D3 receptor/0.477
4dpdUMPBifunctional dihydrofolate reductase-thymidylate synthase/0.477
2dxdANPNucleoside diphosphate kinase2.7.4.60.475
3q8uADPNucleoside diphosphate kinase/0.474
4a83DXCMajor pollen allergen Bet v 1-A/0.474
1z6tADPApoptotic protease-activating factor 1/0.473
4fogC2FThymidylate synthase ThyA/0.473
4g2i0VQVitamin D3 receptor/0.473
3acy702Dehydrosqualene synthase/0.472
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.471
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.471
3gwdNAPCyclohexanone monooxygenase/0.468
3hk1B64Fatty acid-binding protein, adipocyte/0.468
4ia7BIVVitamin D3 receptor A/0.468
4j0v1H7Beta-secretase 13.4.23.460.468
4rupH97Vitamin D3 receptor A/0.468
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.467
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.466
3dgaUMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.466
4ymgSAMPutative SAM-dependent O-methyltranferase/0.466
4cf7ADPAdenylate kinase/0.465
4f3gKAIGlutamate receptor 3/0.465
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.465
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.465
4jtrIBPAldo-keto reductase family 1 member C2/0.464
2egsSAHDiphthine synthase/0.463
2hb7O1CVitamin D3 receptor/0.463
2v59LZKBiotin carboxylase6.3.4.140.463
1dr5NAPDihydrofolate reductase1.5.1.30.462
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.462
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.462
3vruYS3Vitamin D3 receptor/0.462
2j62GSZO-GlcNAcase NagJ/0.461
3w0jT08Vitamin D3 receptor/0.461
4gtp7TPProtein farnesyltransferase subunit beta2.5.1.580.461
4ytnFD8Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.461
4ytnFD8Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial/0.461
4ytnFD8Succinate dehydrogenase cytochrome b560/0.461
1g28FMNPHY3/0.460
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.460
3qczANPDihydrofolate synthase/folylpolyglutamate synthase/0.460
3up3XCAaceDAF-12/0.460
4g1z0VPVitamin D3 receptor A/0.460
4iteTEYVitamin D3 receptor/0.460
3odkODKPeptidyl-prolyl cis-trans isomerase NIMA-interacting 15.2.1.80.459
3vrwYS5Vitamin D3 receptor/0.459
4mv4ACPBiotin carboxylase6.3.4.140.459
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.458
3mqe416Prostaglandin G/H synthase 21.14.99.10.458
1ihiIU5Aldo-keto reductase family 1 member C2/0.457
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.457
2egbSAHDiphthine synthase/0.457
2rlcCHDCholoylglycine hydrolase3.5.1.240.457
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.457
4mka2AYGenome polyprotein2.7.7.480.457
4p9dTMPDeoxycytidylate deaminase/0.457
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3wv7ADPHmd co-occurring protein HcgE/0.455
4eilUMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
4g2h0VQVitamin D3 receptor A/0.455
4gukP2GNeuronal calcium sensor 1/0.455
4l1xSTRAldo-keto reductase family 1 member C2/0.455
5agyGTBTau class glutathione S-transferase/0.455
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
1ld8U49Protein farnesyltransferase subunit beta2.5.1.580.454
3af0GDPPantothenate kinase2.7.1.330.454
4dk70KSOxysterols receptor LXR-beta/0.454
5hi6MTXDihydrofolate reductase/0.454
2g8dUMPThymidylate synthase/0.453
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.453
4qzuRTLRetinol-binding protein 2/0.453
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.452
1zdwFLVPrenyltransferase/0.452
2wdqCBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.452
2wdqCBESuccinate dehydrogenase cytochrome b556 subunit/0.452
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.452
4eb4UMPThymidylate synthase2.1.1.450.452
4i4z2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.452
1wngSAHDiphthine synthase/0.451
2glrGTXGlutathione S-transferase P 12.5.1.180.451
3sj7NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative/0.451
4biwANPSensor histidine kinase CpxA/0.451
4dbs0HVAldo-keto reductase family 1 member C3/0.451
4foxUMPThymidylate synthase ThyA/0.451
1njcDCMThymidylate synthase/0.450
1opbRETRetinol-binding protein 2/0.450
1pq944BOxysterols receptor LXR-beta/0.450
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.450
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.450
4a81DXCMajor pollen allergen Bet v 1-A/0.450
4bfzZVZPantothenate kinase2.7.1.330.450
4earIM5Purine nucleoside phosphorylase2.4.2.10.450
1dr3TAPDihydrofolate reductase1.5.1.30.449
1pqc444Oxysterols receptor LXR-beta/0.449
2dxxSAHDiphthine synthase/0.449
2hamC33Vitamin D3 receptor/0.449
3juqAJDPhenazine biosynthesis protein A/B/0.449
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
5e8ySTUTGF-beta receptor type-22.7.11.300.449
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.448
3vrvYSDVitamin D3 receptor/0.448
4b69FADL-ornithine N(5)-monooxygenase/0.448
4einNOHThymidylate synthase2.1.1.450.448
4mkgAP5Adenylate kinase/0.448
4u7wNDPMxaA/0.448
1s07PLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.447
1s19MC9Vitamin D3 receptor/0.447
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.447
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3u4o08EGenome polyprotein2.7.7.480.447
3uthGDUUDP-galactopyranose mutase/0.447
4bfyZVYPantothenate kinase2.7.1.330.447
1rf7DHFDihydrofolate reductase1.5.1.30.446
1zhaPEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.446
2owgSAHDiphthine synthase/0.446
3cxw7CPSerine/threonine-protein kinase pim-12.7.11.10.446
3fqk79ZGenome polyprotein2.7.7.480.446
3p0fBAUUridine phosphorylase 22.4.2.30.446
3p5pA3CTaxadiene synthase4.2.3.170.446
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
4kwhNAPReductase homolog/0.446
5djtFMNNPH1-2/0.446
1cqp803Integrin alpha-L/0.445
2g89UMPThymidylate synthase/0.445
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.445
3r43ID8Aldo-keto reductase family 1 member C3/0.445
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4k9nTZDBenzoylformate decarboxylase4.1.1.70.445
1szgFNSCytochrome b2, mitochondrial1.1.2.30.444
2wu5CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.444
2wu5CBESuccinate dehydrogenase cytochrome b556 subunit/0.444
2yoj8Y6Genome polyprotein2.7.7.480.444
3oafOAGDihydrofolate reductase1.5.1.30.444
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.444
4mkhAP5Adenylate kinase/0.444
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
2j09FMNDeoxyribodipyrimidine photo-lyase4.1.99.30.443
2ycnP61Tyrosine phenol-lyase4.1.99.20.443
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.443
1dr2TAPDihydrofolate reductase1.5.1.30.442
1jq5NADGlycerol dehydrogenase1.1.1.60.442
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.442
2ftoCB3Thymidylate synthase/0.442
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
2v3oI26Prothrombin3.4.21.50.442
3csdEMOPutative ketoacyl reductase1.3.10.442
3gieACPSensor histidine kinase DesK2.7.13.30.442
3mauPLRPutative sphingosine-1-phosphate lyase/0.442
3up0D7SaceDAF-12/0.442
4iae1DXAlr2278 protein/0.442
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.442
1tvrTB9Gag-Pol polyprotein2.7.7.490.441
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.441
1xdpATPPolyphosphate kinase/0.441
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.441
2eldSAHDiphthine synthase/0.441
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.441
2xpc051UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
3i0aDBHNeutrophil gelatinase-associated lipocalin/0.441
3keuATPPyridoxal kinase2.7.1.350.441
3slkNDPPolyketide synthase extender module 2/0.441
3wqmB29Diterpene synthase3.1.7.80.441
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.441
1a4lDCFAdenosine deaminase3.5.4.40.440
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.440
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.440
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.440
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.440
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.440
1re0AFBADP-ribosylation factor 1/0.440
1re0AFBARF guanine-nucleotide exchange factor 1/0.440
1tqf32PBeta-secretase 13.4.23.460.440
1x7gNAPPutative ketoacyl reductase1.3.10.440
2an9GDPGuanylate kinase2.7.4.80.440
2c31ADPOxalyl-CoA decarboxylase4.1.1.80.440
2e0nSAHPrecorrin-2 C20-methyltransferase/0.440
2e7rSAHDiphthine synthase/0.440
2jlcTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.440
2w71L23Biotin carboxylase6.3.4.140.440
3gonANPPhosphomevalonate kinase/0.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4lzwTHMUridine phosphorylase/0.440