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
4bmzMTAAminodeoxyfutalosine nucleosidase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4bmzMTAAminodeoxyfutalosine nucleosidase/1.000
3eeiMTM5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.572
1y6rMTM5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase3.2.2.90.569
1zosMTM5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.555
4x24TDI5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.528
1y6qTDI5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase3.2.2.90.515
1o6qR17Squalene--hopene cyclase4.2.1.1290.500
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.493
1jtqLY3Thymidylate synthase/0.488
1synF89Thymidylate synthase/0.487
1nc1MTH5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase3.2.2.90.485
2yisI46Mitogen-activated protein kinase 14/0.484
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.483
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.483
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.479
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.477
1zq5E04Aldo-keto reductase family 1 member C3/0.475
2uuk897Prothrombin3.4.21.50.474
4eh8IRGMitogen-activated protein kinase 14/0.473
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.472
4jv41ORcAMP-dependent protein kinase type I-alpha regulatory subunit/0.472
4zthGG5Mitogen-activated protein kinase 14/0.472
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.471
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.470
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.469
2fzjDH3Dihydrofolate reductase1.5.1.30.469
3c36KAIGlutamate receptor ionotropic, kainate 1/0.469
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.468
1d3dBZTProthrombin3.4.21.50.468
3pg3DG7Mitogen-activated protein kinase 14/0.468
1dlsMTXDihydrofolate reductase1.5.1.30.467
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.467
3anmNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.467
1h35R01Squalene--hopene cyclase4.2.1.1290.466
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.466
4fam0SZAldo-keto reductase family 1 member C3/0.466
4kd79DRDihydrofolate reductase1.5.1.30.466
4pnmNU1Tankyrase-22.4.2.300.466
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.465
3zeiAWHO-acetylserine sulfhydrylase/0.465
2c42TPPPyruvate synthase/0.464
1ozqPRFQueuine tRNA-ribosyltransferase2.4.2.290.463
1q4wDQUQueuine tRNA-ribosyltransferase2.4.2.290.463
3qp8HL0Transcriptional activator, LuxR/UhpA family of regulators/0.463
4aoaIK2Beta-phenylalanine transaminase2.6.10.463
1nceCB3Thymidylate synthase/0.461
2bbqPFGThymidylate synthase/0.461
3rl45GPMetallophosphoesterase MPPED23.10.460
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
1tsdF89Thymidylate synthase/0.459
2z2w770Wee1-like protein kinase2.7.10.20.459
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.459
4eh4IRGMitogen-activated protein kinase 14/0.459
1f28F89Thymidylate synthase2.1.1.450.458
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.458
3dp9BIG5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.458
3njoPYVAbscisic acid receptor PYR1/0.458
3roc29BMitogen-activated protein kinase 14/0.458
1mvtDTMDihydrofolate reductase1.5.1.30.457
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
2xtbKRMAdenosine kinase, putative/0.457
4eh2IRGMitogen-activated protein kinase 14/0.457
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.457
2hzqSTRApolipoprotein D/0.456
3ojgHL4Phosphotriesterase/0.456
4wkbTDI5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.456
1h36R88Squalene--hopene cyclase4.2.1.1290.455
1ohjCOPDihydrofolate reductase1.5.1.30.455
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.455
1x2hLPALipoate-protein ligase A6.3.1.200.455
2e1zB4PPropionate kinase/0.455
2wksCB63-dehydroquinate dehydratase4.2.1.100.455
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.455
1dr3TAPDihydrofolate reductase1.5.1.30.454
1ygjRMCPyridoxal kinase2.7.1.350.454
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.454
3af1GDPPantothenate kinase2.7.1.330.454
3gc4AAQQueuine tRNA-ribosyltransferase2.4.2.290.454
3hv3R49Mitogen-activated protein kinase 14/0.454
3p2oNADBifunctional protein FolD/0.454
4kbn25UDihydrofolate reductase1.5.1.30.454
1sjwNGVNogalonic acid methyl ester cyclase/0.453
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.453
3n0hTOPDihydrofolate reductase1.5.1.30.453
3ns2PYVAbscisic acid receptor PYL2/0.453
3vf60H6Glucokinase2.7.1.20.453
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.453
4l8vNAPInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.453
4pl9ADPEthylene receptor 1/0.453
2gevCOKPantothenate kinase2.7.1.330.452
3cqeP91Wee1-like protein kinase2.7.10.20.452
3k3iI46Mitogen-activated protein kinase 14/0.452
4az0S61Lysosomal protective protein3.4.16.50.452
4dsbA8SAbscisic acid receptor PYL3/0.452
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4rh10TTSpore photoproduct lyase/0.452
1drfFOLDihydrofolate reductase1.5.1.30.451
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1t7o152Carnitine O-acetyltransferase2.3.1.70.451
3c3eFO12-phospho-L-lactate transferase/0.451
3gcq1BUMitogen-activated protein kinase 14/0.451
3hf6LX0Tryptophan 5-hydroxylase 11.14.16.40.451
3n87N873-dehydroquinate dehydratase4.2.1.100.451
4omaLCSMethionine gamma-lyase/0.451
2c97JCL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
3ge7AFQQueuine tRNA-ribosyltransferase2.4.2.290.450
4aqlTXCGuanine deaminase3.5.4.30.450
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.449
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
3r43ID8Aldo-keto reductase family 1 member C3/0.449
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
4dhyS41Glucokinase2.7.1.20.449
2in6839Wee1-like protein kinase2.7.10.20.448
2psjCEIRenilla-luciferin 2-monooxygenase1.13.12.50.448
3s41S41Glucokinase2.7.1.20.448
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.448
4gh30EVQueuine tRNA-ribosyltransferase2.4.2.290.448
1gky5GPGuanylate kinase2.7.4.80.447
1ohkCOPDihydrofolate reductase1.5.1.30.447
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.447
2y60M8FIsopenicillin N synthase1.21.3.10.447
3hllI46Mitogen-activated protein kinase 14/0.447
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.447
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4g95OAGDihydrofolate reductase1.5.1.30.447
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.447
4kak06UDihydrofolate reductase1.5.1.30.447
4qii2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.447
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.446
1fmlRTLRetinol dehydratase/0.446
1fvpFMANon-fluorescent flavoprotein/0.446
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.446
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2j7cIDEBeta-glucosidase A3.2.1.210.446
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.446
2z3uCRRCytochrome P450/0.446
3l3rOAGDihydrofolate reductase1.5.1.30.446
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
4fhf0TTSpore photoproduct lyase/0.446
4lsaBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.446
1jomFFODihydrofolate reductase1.5.1.30.445
1ndyFR3Adenosine deaminase3.5.4.40.445
1z71L17Prothrombin3.4.21.50.445
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3eta351Insulin receptor2.7.10.10.445
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.445
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.445
4m6kFOLDihydrofolate reductase1.5.1.30.445
1dhfFOLDihydrofolate reductase1.5.1.30.444
1kmvLIIDihydrofolate reductase1.5.1.30.444
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2braFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.444
2c9bPUG6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2vcmM11Isopenicillin N synthase1.21.3.10.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
1blzACVIsopenicillin N synthase1.21.3.10.443
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.443
1hfrMOTDihydrofolate reductase1.5.1.30.443
1pq944BOxysterols receptor LXR-beta/0.443
1s3vTQDDihydrofolate reductase1.5.1.30.443
2ji9ADPOxalyl-CoA decarboxylase4.1.1.80.443
2mokFMNFlavodoxin 1/0.443
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.443
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.443
3ghvGHCDihydrofolate reductase1.5.1.30.443
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.443
3hl7I46Mitogen-activated protein kinase 14/0.443
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.443
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.443
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.443
4kebFOLDihydrofolate reductase1.5.1.30.443
5agyGTBTau class glutathione S-transferase/0.443
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.442
1t0iFMNNAD(P)H-dependent FMN reductase LOT6/0.442
1uhlMEIRetinoic acid receptor RXR-beta/0.442
2c3p1TPPyruvate synthase/0.442
2og81N8Tyrosine-protein kinase Lck2.7.10.20.442
3f3y4OABile salt sulfotransferase2.8.2.140.442
3k4551PDihydrofolate reductase1.5.1.30.442
3nu03TUDihydrofolate reductase1.5.1.30.442
4kfj1R0Dihydrofolate reductase1.5.1.30.442
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4tjy3GNTankyrase-22.4.2.300.442
1q63AIQQueuine tRNA-ribosyltransferase2.4.2.290.441
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.441
3p9tTCLRepressor/0.441
3qp6HL6Transcriptional activator, LuxR/UhpA family of regulators/0.441
4ixgIXGDihydrofolate reductase1.5.1.30.441
1disBDMDihydrofolate reductase1.5.1.30.440
1t4v14AProthrombin3.4.21.50.440
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.440
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.440
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.440
3l77NJPShort-chain alcohol dehydrogenase/0.440
4dliIRGMitogen-activated protein kinase 14/0.440
4h7zGUNQueuine tRNA-ribosyltransferase2.4.2.290.440
4ksp1SUSerine/threonine-protein kinase B-raf2.7.11.10.440
5bp9SAHPutative methyltransferase protein/0.440