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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
4boyNADGlyceraldehyde-3-phosphate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/1.000
1rm4NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.664
3zcxNADGlyceraldehyde-3-phosphate dehydrogenase/0.663
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.625
2dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.624
1jn0NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.622
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.620
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.620
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.616
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.613
2pkrNDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.612
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.611
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.606
1nboNADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.605
1rm3NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.602
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.600
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.595
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.595
2d2iNAPGlyceraldehyde-3-phosphate dehydrogenase/0.593
3gnqNADGlyceraldehyde-3-phosphate dehydrogenase/0.587
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.586
1vc2NADGlyceraldehyde-3-phosphate dehydrogenase/0.585
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.583
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.583
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.577
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.567
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.565
3pymNADGlyceraldehyde-3-phosphate dehydrogenase 31.2.1.120.559
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.547
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.546
2b4rNADGlyceraldehyde-3-phosphate dehydrogenase/0.546
1ihxSNDGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.545
3l0dNADGlyceraldehyde-3-phosphate dehydrogenase/0.541
1gadNADGlyceraldehyde-3-phosphate dehydrogenase A/0.539
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.538
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase/0.536
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.532
1cerNADGlyceraldehyde-3-phosphate dehydrogenase/0.523
2vynNADGlyceraldehyde-3-phosphate dehydrogenase A/0.519
1vsvNADGlyceraldehyde-3-phosphate dehydrogenase/0.511
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.481
1ihyAPRGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.475
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.474
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.466
3gobHXXDdmC/0.466
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.466
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.465
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.464
1owmFADDeoxyribodipyrimidine photo-lyase4.1.99.30.464
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.464
4q73FADBifunctional protein PutA/0.462
4uymVOR14-alpha sterol demethylase Cyp51B/0.460
3s79ASDAromatase1.14.14.140.458
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.458
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.456
4bqh9VUUDP-N-acetylglucosamine pyrophosphorylase, putative/0.455
1bwsNDPGDP-L-fucose synthase/0.454
1iqrFADDeoxyribodipyrimidine photo-lyase4.1.99.30.453
1o9bNAIQuinate/shikimate dehydrogenase/0.452
3a1nNADNDP-sugar epimerase/0.452
2givACOHistone acetyltransferase KAT8/0.451
4gk3L87Ephrin type-A receptor 32.7.10.10.451
4yaoFMNNADPH--cytochrome P450 reductase/0.451
4nxuADPMitochondrial dynamics protein MID51/0.450
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1j0xNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.449
2xyuQ9GEphrin type-A receptor 42.7.10.10.449
2y6o1N1Ephrin type-A receptor 42.7.10.10.449
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
1pdhFASp-hydroxybenzoate hydroxylase/0.448
2ft9CHDFatty acid-binding protein 2, liver/0.448
3ad9NADSubunit alpha of sarocosine oxidase/0.448
3ru7NADUDP-N-acetylglucosamine 4-epimerase/0.448
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
4gk2L66Ephrin type-A receptor 32.7.10.10.448
1dhiMTXDihydrofolate reductase1.5.1.30.447
1owoFADDeoxyribodipyrimidine photo-lyase4.1.99.30.447
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.447
4f07FADStyrene monooxygenase component 2/0.447
3bheBZNGag-Pol polyprotein3.4.23.160.446
3zewSTUEphrin type-B receptor 42.7.10.10.446
4nmdFDABifunctional protein PutA/0.446
3bgbLJGGag-Pol polyprotein3.4.23.160.445
3il1B5DGlutamate receptor 2/0.445
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4i6gFADCryptochrome-2/0.445
2gn8NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.444
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.444
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.444
1tehNADAlcohol dehydrogenase class-31.1.1.10.443
4b4oNDPEpimerase family protein SDR39U1/0.443
1adfTADAlcohol dehydrogenase E chain1.1.1.10.442
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1owpFADDeoxyribodipyrimidine photo-lyase4.1.99.30.442
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.442
2y0mACOHistone acetyltransferase KAT8/0.442
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
1bw9NADPhenylalanine dehydrogenase/0.441
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.441
1t0lNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.441
1z7yAA5Cysteine synthase 12.5.1.470.441
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.441
2dq7STUTyrosine-protein kinase Fyn2.7.10.20.441
2y4gTIRTamL/0.441
3u9eCOALmo1369 protein/0.441
4eutBX7Serine/threonine-protein kinase TBK12.7.11.10.441
1np7FADCryptochrome DASH/0.440
2ejvNADL-threonine 3-dehydrogenase/0.440
3b895GP16S rRNA methylase/0.440
4c58824Cyclin-G-associated kinase2.7.11.10.440