sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4u0k | 744 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4u0k | 744 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.000 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.700 | |
| 4tzk | 641 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.664 | |
| 4trj | 665 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.661 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.619 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.597 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.582 | |
| 5cp8 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.580 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.576 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.554 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.549 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.536 | |
| 5coq | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.532 | |
| 3uic | 09T | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.509 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.507 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.501 | |
| 3fnf | JPM | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.495 | |
| 4u0j | 566 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.492 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.490 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.486 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.484 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.482 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.481 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.480 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.479 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.478 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.475 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.474 | |
| 1fml | RTL | Retinol dehydratase | / | 0.471 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.471 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.471 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.471 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.471 | |
| 4l8u | 9AZ | Serum albumin | / | 0.469 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.469 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.468 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.468 | |
| 1d3g | BRE | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.467 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.467 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1zsn | TN2 | Enoyl-ACP reductase | / | 0.466 | |
| 3fne | 8PC | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.466 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.466 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.466 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.465 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.464 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.464 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.464 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.462 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.462 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.461 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.460 | |
| 1z69 | F42 | 5,10-methylenetetrahydromethanopterin reductase | / | 0.460 | |
| 1zxl | JP1 | Enoyl-ACP reductase | / | 0.460 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.460 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.460 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.459 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.459 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.458 | |
| 3dej | RXC | Caspase-3 | 3.4.22.56 | 0.458 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.458 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 4bzo | 676 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.457 | |
| 1sqi | 869 | 4-hydroxyphenylpyruvate dioxygenase | / | 0.456 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.456 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.456 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.455 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.455 | |
| 1hk5 | T44 | Serum albumin | / | 0.454 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.454 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.454 | |
| 4kio | G5K | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.454 | |
| 1e7a | PFL | Serum albumin | / | 0.453 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.453 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.453 | |
| 3eek | 53S | Uncharacterized protein | / | 0.453 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 3zkp | ERB | Erythromycin C-12 hydroxylase | 1.14.13.154 | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.453 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.453 | |
| 3b9l | AZZ | Serum albumin | / | 0.452 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.451 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.451 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.451 | |
| 4lb2 | DM5 | Serum albumin | / | 0.451 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.451 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.450 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.450 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.450 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.449 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.449 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.449 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.449 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.449 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.448 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.448 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.447 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.447 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.447 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.447 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.446 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.446 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3lu8 | IQX | Serum albumin | / | 0.446 | |
| 3u2l | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.446 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.446 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.446 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.446 | |
| 5dp2 | NAP | CurF | / | 0.446 | |
| 1osv | CHC | Bile acid receptor | / | 0.445 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.445 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.445 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.445 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.444 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.444 | |
| 1lce | TMF | Thymidylate synthase | / | 0.444 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.444 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.444 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2nn7 | M29 | Carbonic anhydrase 1 | 4.2.1.1 | 0.443 | |
| 2w6m | OA1 | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3bhr | THG | Thymidylate synthase | / | 0.443 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.443 | |
| 3bzu | A21 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.443 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.443 | |
| 1kvo | OAP | Phospholipase A2, membrane associated | / | 0.442 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.442 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.442 | |
| 2wle | COA | Polysialic acid O-acetyltransferase | / | 0.442 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.442 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.441 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.441 | |
| 4b1f | KRH | Glutamate racemase | / | 0.441 | |
| 4fny | I3K | ALK tyrosine kinase receptor | 2.7.10.1 | 0.441 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.441 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.440 | |
| 2bxq | IMN | Serum albumin | / | 0.440 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2dr3 | ADP | UPF0273 protein PH0284 | / | 0.440 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.440 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.440 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.440 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.440 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4n70 | 2HX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.440 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.440 |