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 |
|---|---|---|---|
| 3fzw | EQU | Steroid Delta-isomerase | 5.3.3.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3fzw | EQU | Steroid Delta-isomerase | 5.3.3.1 | 1.000 | |
| 1e3v | DXC | Steroid Delta-isomerase | 5.3.3.1 | 0.638 | |
| 1e3r | AND | Steroid Delta-isomerase | 5.3.3.1 | 0.583 | |
| 3ows | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.574 | |
| 3owy | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.574 | |
| 1ogx | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.565 | |
| 3ipt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.562 | |
| 1gs3 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.521 | |
| 1oh0 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.510 | |
| 1cqs | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.497 | |
| 1w6y | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.494 | |
| 1qjg | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.491 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.487 | |
| 3owu | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.482 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.481 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.481 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.480 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.479 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.476 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.475 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.475 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.474 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.473 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.472 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 2f8p | CEI | Obelin | / | 0.470 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.469 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.469 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.468 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.468 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.467 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.466 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.466 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.466 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.465 | |
| 1oho | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.465 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.464 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.464 | |
| 4guk | P2G | Neuronal calcium sensor 1 | / | 0.464 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3up3 | XCA | aceDAF-12 | / | 0.463 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.463 | |
| 2bxo | OPB | Serum albumin | / | 0.462 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1eio | GCH | Gastrotropin | / | 0.461 | |
| 2bxq | IMN | Serum albumin | / | 0.461 | |
| 4ict | 1ED | Mycocyclosin synthase | 1.14.21.9 | 0.461 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.460 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.459 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.459 | |
| 1jut | LYD | Thymidylate synthase | / | 0.458 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.458 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.458 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.458 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.457 | |
| 2xvw | 9NR | Serum albumin | / | 0.457 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.456 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.456 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.455 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.455 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.455 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.455 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.454 | |
| 3r6p | A8S | Abscisic acid receptor PYL10 | / | 0.454 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.454 | |
| 5iqe | GNP | Bifunctional AAC/APH | 2.3.1 | 0.454 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.453 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.453 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.453 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.453 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.453 | |
| 3vgn | FNN | Steroid Delta-isomerase | 5.3.3.1 | 0.453 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.452 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.452 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.452 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.451 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.451 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.451 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.451 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.451 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.450 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4l8u | 9AZ | Serum albumin | / | 0.450 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.449 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1pw6 | FRB | Interleukin-2 | / | 0.449 | |
| 1tys | TMP | Thymidylate synthase | / | 0.449 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3p9t | TCL | Repressor | / | 0.449 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.449 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.449 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.448 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.448 | |
| 3b9l | AZZ | Serum albumin | / | 0.448 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.448 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.448 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.448 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.448 | |
| 4k5y | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.448 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.447 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.447 | |
| 2f0y | 3MN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.447 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.447 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 1jxz | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.446 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.446 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.446 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.446 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.446 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4l9q | 9TP | Serum albumin | / | 0.446 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.445 | |
| 2gpv | OHT | Estrogen-related receptor gamma | / | 0.445 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.445 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.445 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.445 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.445 | |
| 4j7x | SAS | Sepiapterin reductase | 1.1.1.153 | 0.445 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.445 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.445 | |
| 5d5b | CAU | Beta-2 adrenergic receptor | / | 0.445 | |
| 1wl4 | COA | Acetyl-CoA acetyltransferase, cytosolic | 2.3.1.9 | 0.444 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.444 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.444 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.444 | |
| 3eku | CY9 | Actin-5C | / | 0.444 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.444 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.444 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4b1i | A8P | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.444 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.444 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 1m52 | P17 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.443 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.443 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.443 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.443 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.443 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.443 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.443 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.443 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.443 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.443 | |
| 4p2l | FAD | Sulfhydryl oxidase 1 | 1.8.3.2 | 0.443 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.443 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 1nja | DCM | Thymidylate synthase | / | 0.442 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.442 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.442 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.442 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.442 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.442 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.442 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.441 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.441 | |
| 3up0 | D7S | aceDAF-12 | / | 0.441 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.441 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 4zas | TYD | CalS13 | / | 0.441 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2xtb | KRM | Adenosine kinase, putative | / | 0.440 | |
| 3cyz | 9OD | Pheromone-binding protein ASP1 | / | 0.440 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.440 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.440 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.440 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.440 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.440 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.440 |