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
5dx8SFGHistone-arginine methyltransferase CARM1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
5dx8SFGHistone-arginine methyltransferase CARM1/1.000
5dxaSFGHistone-arginine methyltransferase CARM1/0.681
5dxjSFGHistone-arginine methyltransferase CARM1/0.659
5dx1SFGHistone-arginine methyltransferase CARM1/0.656
2y1wSFGHistone-arginine methyltransferase CARM1/0.628
5dwqSFGHistone-arginine methyltransferase CARM1/0.618
2y1xSAHHistone-arginine methyltransferase CARM1/0.614
3b3fSAHHistone-arginine methyltransferase CARM1/0.612
1f3lSAHProtein arginine N-methyltransferase 3/0.581
4c03SFGProtein arginine N-methyltransferase 6/0.530
2bzgSAHThiopurine S-methyltransferase2.1.1.670.512
5dstSAHProtein arginine N-methyltransferase 82.1.10.507
1p4mADPRiboflavin kinase2.7.1.260.505
3up3XCAaceDAF-12/0.502
4kwcSAHMethyltransferase domain family/0.500
3bgvSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.495
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.492
2a14SAHIndolethylamine N-methyltransferase2.1.1.490.490
4e2xSAHMethyltransferase/0.490
3nwb659Catechol O-methyltransferase2.1.1.60.488
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.487
3lcvSAM16S rRNA (guanine(1405)-N(7))-methyltransferase2.1.1.1790.478
2v74SAHHistone-arginine methyltransferase CARM1/0.477
3up0D7SaceDAF-12/0.477
1rkhVD2Vitamin D3 receptor/0.474
2bn4FADNADPH--cytochrome P450 reductase/0.474
4fgzSAHPhosphoethanolamine N-methyltransferase/0.473
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.471
5ekuSAHArginine N-methyltransferase, putative/0.471
3qakUKAAdenosine receptor A2a/0.471
1n06ADPRiboflavin kinase2.7.1.260.470
3t7tSAHUncharacterized protein/0.470
5eghPCEctonucleotide pyrophosphatase/phosphodiesterase family member 6/0.470
4ft4SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.468
4necSAHPutative SAM-dependent methyltransferase/0.467
2r8pT6FTransketolase 1/0.466
5ccxSAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A2.1.1.2200.465
1pq944BOxysterols receptor LXR-beta/0.462
2y48FADLysine-specific histone demethylase 1A10.462
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.462
5je4SAHMethyl transferase/0.461
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.460
2hcdBIVVitamin D3 receptor A/0.460
4iteTEYVitamin D3 receptor/0.460
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.459
1dr3TAPDihydrofolate reductase1.5.1.30.458
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.458
3qvsNADMyo-inositol-1-phosphate synthase (Ino1)/0.458
4r6xSAHPhosphoethanolamine N-methyltransferase/0.458
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.457
3kpjSAHPhenylethanolamine N-methyltransferase2.1.1.280.457
1nbiSAMGlycine N-methyltransferase2.1.1.200.456
1pqc444Oxysterols receptor LXR-beta/0.456
2zvcSAHPrecorrin-3 C17-methyltransferase/0.456
2zw9SAMtRNA wybutosine-synthesizing protein 42.1.1.2900.456
3ou6SAMSAM-dependent methyltransferase/0.456
4ax8SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.456
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.456
5je3SAHMethyl transferase/0.456
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.455
1gpuTHDTransketolase 12.2.1.10.454
1n08ADPRiboflavin kinase2.7.1.260.454
1skmSAHModification methylase HhaI2.1.1.370.454
4twnB96Ephrin type-A receptor 32.7.10.10.454
1zdwFLVPrenyltransferase/0.453
2zl9VDAVitamin D3 receptor/0.453
3ou7SAMSAM-dependent methyltransferase/0.453
3vrwYS5Vitamin D3 receptor/0.453
4hy6FJ1Heat shock protein HSP 90-alpha/0.453
4rtoSFGDNA adenine methylase2.1.1.720.453
3uj7SAMPhosphoethanolamine N-methyltransferase/0.452
1dr3HBIDihydrofolate reductase1.5.1.30.451
1g9rUPFLgtC/0.451
2i62SAHNicotinamide N-methyltransferase2.1.1.10.451
3lhdSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2190.451
3tljSAHUncharacterized protein/0.451
2hb7O1CVitamin D3 receptor/0.450
1pw1HELD-alanyl-D-alanine carboxypeptidase3.4.16.40.449
3uj8SFGPhosphoethanolamine N-methyltransferase/0.449
4w6z8IDAlcohol dehydrogenase 11.1.1.10.449
4y1bNAPAntE/0.449
1trkTPPTransketolase 12.2.1.10.448
1yhjR6CPyridoxal kinase2.7.1.350.448
2hamC33Vitamin D3 receptor/0.448
3h4vNAPPteridine reductase 11.5.1.330.448
4g95OAGDihydrofolate reductase1.5.1.30.448
4xba5GPAprataxin-like protein30.448
5epeSAHUncharacterized protein/0.448
1af7SAHChemotaxis protein methyltransferase2.1.1.800.447
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.447
1upw444Oxysterols receptor LXR-beta/0.447
2zynBCDPeriplasmic binding protein/0.447
4m37SAHProtein arginine N-methyltransferase 72.1.10.447
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.446
1p8dCO1Oxysterols receptor LXR-beta/0.446
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.446
2r0pK2CPutative FAD-monooxygenase/0.446
3cgcCOACoenzyme A disulfide reductase/0.446
3gtsD3MDdmC/0.446
5fhqDNCCatechol O-methyltransferase2.1.1.60.446
1nhkCMPNucleoside diphosphate kinase2.7.4.60.445
2b8tTHMThymidine kinase/0.445
2is0I03Beta-secretase 13.4.23.460.445
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.445
1gky5GPGuanylate kinase2.7.4.80.444
2iidFADL-amino-acid oxidase1.4.3.20.444
2qcuFADAerobic glycerol-3-phosphate dehydrogenase1.1.5.30.444
2yg6FADPutrescine oxidase/0.444
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.444
1db56INPhospholipase A2, membrane associated/0.443
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.443
3afhGSUGlutamate--tRNA ligase 2/0.443
3tm4SAMUncharacterized protein/0.443
4krhSAMPhosphoethanolamine N-methyltransferase 2/0.443
4u7wNDPMxaA/0.443
4ymgSAMPutative SAM-dependent O-methyltranferase/0.443
5icfSAH(S)-norcoclaurine 6-O-methyltransferase/0.443
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.442
2uywBTNAvd protein/0.442
3ozsOZSCatechol O-methyltransferase2.1.1.60.442
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.442
3w0aDS5Vitamin D3 receptor/0.442
3wv7ADPHmd co-occurring protein HcgE/0.442
4m6l21VDihydrofolate reductase1.5.1.30.442
1lkeDOGBilin-binding protein/0.441
2harOCCVitamin D3 receptor/0.441
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.441
3w5tLHPVitamin D3 receptor/0.441
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.440
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.440
1reoFADL-amino-acid oxidase1.4.3.20.440
1s19MC9Vitamin D3 receptor/0.440
2geuCOKPantothenate kinase2.7.1.330.440