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 |
|---|---|---|---|
| 1td2 | PXL | Pyridoxal kinase PdxY |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1td2 | PXL | Pyridoxal kinase PdxY | / | 1.000 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.501 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.473 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.470 | |
| 4dc3 | 2FA | Putative adenosine kinase | / | 0.469 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.467 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.466 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.466 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.466 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.466 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.466 | |
| 2c3l | IDZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.465 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.465 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.464 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.464 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.463 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.463 | |
| 2itp | AEE | Epidermal growth factor receptor | 2.7.10.1 | 0.462 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.462 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.462 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.461 | |
| 1l2o | ADP | Myosin heavy chain, striated muscle | / | 0.460 | |
| 2wmu | ZYU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.459 | |
| 2pmn | K51 | Protein kinase 7 | / | 0.458 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.458 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.457 | |
| 4fsr | HKC | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.456 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.456 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 0.456 | |
| 1snu | STU | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.455 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.455 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.455 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.455 | |
| 1bpj | UMP | Thymidylate synthase | / | 0.454 | |
| 2cgv | 3B3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.454 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.454 | |
| 3ag9 | A02 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 4fsw | HK6 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 4ftt | 6HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 1g6n | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.453 | |
| 3q0u | LL3 | HTH-type transcriptional regulator EthR | / | 0.453 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.452 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.452 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.452 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.452 | |
| 1qvr | ANP | Chaperone protein ClpB | / | 0.451 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2y3p | SM8 | DNA gyrase subunit A | / | 0.451 | |
| 2ydi | YDI | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.451 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.451 | |
| 4jq7 | KJQ | Epidermal growth factor receptor | 2.7.10.1 | 0.451 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.451 | |
| 4u0o | MTA | Lipoyl synthase 2 | / | 0.451 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.450 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 2xk9 | XK9 | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.450 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.450 | |
| 1bcp | ATP | Pertussis toxin subunit 4 | / | 0.449 | |
| 1bcp | ATP | Pertussis toxin subunit 5 | / | 0.449 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.449 | |
| 1h47 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.449 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.449 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.449 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.449 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.449 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2brn | DF1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.448 | |
| 2z50 | 028 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.448 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.448 | |
| 3nuu | JOZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.447 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1wl4 | COA | Acetyl-CoA acetyltransferase, cytosolic | 2.3.1.9 | 0.447 | |
| 2brg | DFY | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.447 | |
| 2qhm | 7CS | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2r5n | TPP | Transketolase 1 | / | 0.447 | |
| 2vz6 | FEF | Calcium/calmodulin-dependent protein kinase type II subunit alpha | 2.7.11.17 | 0.447 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.447 | |
| 2ym7 | YM7 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 4akn | S5B | Bromodomain-containing protein 2 | / | 0.447 | |
| 4brx | KGW | Focal adhesion kinase 1 | 2.7.10.2 | 0.447 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 4qos | ADP | Psp operon transcriptional activator | / | 0.447 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.447 | |
| 1qr0 | COA | 4'-phosphopantetheinyl transferase sfp | 2.7.8 | 0.446 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.446 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.446 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.446 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.446 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.446 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.446 | |
| 4ft5 | H2K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4jr3 | KJR | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.445 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 3ryp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.445 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 4fta | H5K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4h0n | SAH | Dnmt2 | / | 0.445 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.444 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.444 | |
| 2brh | DFW | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.444 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.444 | |
| 2rc4 | ACO | Histone acetyltransferase KAT6A | / | 0.444 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.444 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 2ym4 | 4YM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.443 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.443 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.443 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.443 | |
| 1rw8 | 580 | TGF-beta receptor type-1 | 2.7.11.30 | 0.442 | |
| 2ccu | 2D9 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2fav | APR | Nonstructural polyprotein pp1a | / | 0.442 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.442 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.442 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.442 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.442 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.442 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.442 | |
| 4j1p | 1K0 | Bromodomain-containing protein 2 | / | 0.442 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.442 | |
| 4umx | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.442 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1uu3 | LY4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2ym8 | YM8 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.441 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.441 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.441 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1phk | ATP | Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform | 2.7.11.19 | 0.440 | |
| 1r6g | 442 | Thyroid hormone receptor beta | / | 0.440 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.440 | |
| 2acw | UPG | Glycosyltransferase | / | 0.440 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2bwg | 5GP | GMP reductase 1 | / | 0.440 | |
| 2iby | COA | Acetyl-CoA acetyltransferase, mitochondrial | 2.3.1.9 | 0.440 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2wtd | ZZK | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.440 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.440 | |
| 4ajj | 88R | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.440 |