sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 5fit | AP2 | Bis(5'-adenosyl)-triphosphatase | 3.6.1.29 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5fit | AP2 | Bis(5'-adenosyl)-triphosphatase | 3.6.1.29 | 1.000 | |
| 3eks | CY9 | Actin-5C | / | 0.506 | |
| 4l4x | NDP | AmphI | / | 0.485 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.484 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.482 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.482 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.476 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.475 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.473 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.471 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.471 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.471 | |
| 1av5 | AP2 | Histidine triad nucleotide-binding protein 1 | 3 | 0.469 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.469 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3eku | CY9 | Actin-5C | / | 0.469 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.468 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.467 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.464 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.463 | |
| 1iiu | RTL | Retinol-binding protein 4 | / | 0.462 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.462 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.461 | |
| 5i2f | BS5 | Histidine triad nucleotide-binding protein 1 | 3 | 0.461 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.460 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.460 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.460 | |
| 2ejz | SAH | Diphthine synthase | / | 0.459 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2yoz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.459 | |
| 1osv | CHC | Bile acid receptor | / | 0.458 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.458 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.458 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.458 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.458 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.457 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.457 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.457 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.457 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.455 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.455 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.455 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.455 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.455 | |
| 4k4e | K4E | Tankyrase-1 | 2.4.2.30 | 0.455 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.455 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.454 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.453 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.452 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.451 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.451 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.451 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.451 | |
| 1avd | BTN | Avidin | / | 0.450 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.450 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.450 | |
| 3gki | CLR | Niemann-Pick C1 protein | / | 0.450 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.450 | |
| 5c4f | UPG | Histo-blood group ABO system transferase | / | 0.450 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.450 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.450 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.449 | |
| 1g6c | IFP | Thiamine-phosphate synthase | / | 0.449 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.449 | |
| 2p4i | MR9 | Angiopoietin-1 receptor | 2.7.10.1 | 0.449 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.449 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.449 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.449 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.449 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.448 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.448 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.448 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.448 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.448 | |
| 4xnh | ACO | N-terminal acetyltransferase A complex subunit NAT5 | 2.3.1 | 0.448 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.447 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.447 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.447 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.447 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.447 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.447 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.447 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.447 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.447 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.447 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 1cm0 | COA | Histone acetyltransferase KAT2B | 2.3.1.48 | 0.446 | |
| 1zdw | FLV | Prenyltransferase | / | 0.446 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.446 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.446 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.446 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.446 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.446 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4bqu | CLR | Japanin | / | 0.446 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 4eqr | COA | Coenzyme A disulfide reductase | / | 0.446 | |
| 4v2g | CTC | Tetracycline repressor protein class D | / | 0.446 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.446 | |
| 5a3b | APR | SIR2 family protein | / | 0.446 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.446 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.445 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1q4t | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.445 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.445 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.445 | |
| 3v1u | HXC | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.445 | |
| 3zm5 | IGM | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4d04 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 5dp2 | NAP | CurF | / | 0.445 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.445 | |
| 1a80 | NDP | 2,5-diketo-D-gluconic acid reductase A | 1.1.1.346 | 0.444 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.444 | |
| 2pa7 | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.444 | |
| 2wme | NAP | NAD/NADP-dependent betaine aldehyde dehydrogenase | / | 0.444 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.444 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.444 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3fmz | 2T1 | Retinol-binding protein 4 | / | 0.444 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.444 | |
| 1fxf | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.443 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.443 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.443 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.443 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.443 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4iah | 1DX | Alr2278 protein | / | 0.443 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.442 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.442 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.442 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.442 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2oj9 | BMI | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.442 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.442 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.442 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.442 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2ay9 | 5PV | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.441 | |
| 2i9p | NAD | 3-hydroxyisobutyrate dehydrogenase, mitochondrial | 1.1.1.31 | 0.441 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.441 | |
| 2uyw | BTN | Avd protein | / | 0.441 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.441 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 2zd1 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 3hky | IX6 | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4bva | T3 | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.441 | |
| 4lt6 | 3AT | Poly(A) polymerase gamma | 2.7.7.19 | 0.441 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.441 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.440 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.440 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 2bhi | SFT | Cytotoxin 3 | / | 0.440 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.440 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2p9h | IPT | Lactose operon repressor | / | 0.440 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.440 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.440 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.440 | |
| 4u07 | ATP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.440 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.440 |