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 |
|---|---|---|---|
| 4mry | CEI | Obelin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4mry | CEI | Obelin | / | 1.000 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.504 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.498 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.484 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.481 | |
| 2f8p | CEI | Obelin | / | 0.478 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.478 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.477 | |
| 2xvv | 9DN | Serum albumin | / | 0.477 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.477 | |
| 3elm | 24F | Collagenase 3 | 3.4.24 | 0.477 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1mlz | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.474 | |
| 4iae | 1DX | Alr2278 protein | / | 0.474 | |
| 4y1b | NAP | AntE | / | 0.474 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.473 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.472 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.471 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.471 | |
| 4mt9 | 2D6 | Tankyrase-1 | 2.4.2.30 | 0.471 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2ea1 | GPG | Ribonuclease I | 3.1.27.6 | 0.468 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.468 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.468 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.468 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.468 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.467 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1qvu | PRL | HTH-type transcriptional regulator QacR | / | 0.466 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.466 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.465 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.464 | |
| 4kxj | P34 | Nucleoprotein | / | 0.464 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.463 | |
| 1srf | MTB | Streptavidin | / | 0.463 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.463 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.463 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
| 1hfr | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.461 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.461 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.461 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.461 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.461 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.460 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.460 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.459 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.458 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.457 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.457 | |
| 2xvw | 9NR | Serum albumin | / | 0.456 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.456 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.456 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 4g8b | HL6 | Alpha/beta hydrolase fold protein | / | 0.456 | |
| 4g8c | C6L | Alpha/beta hydrolase fold protein | / | 0.456 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.456 | |
| 1dtp | APU | Diphtheria toxin | / | 0.455 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1gjr | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.454 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.454 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.454 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.454 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2bxo | OPB | Serum albumin | / | 0.453 | |
| 3tfj | THG | Dimethylsulfonioproprionate demethylase DmdA | 2.1.1.269 | 0.453 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.453 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.453 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.452 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.452 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.452 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.452 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 4phl | PIL | Phosphodiesterase | / | 0.452 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.452 | |
| 1fml | RTL | Retinol dehydratase | / | 0.451 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.451 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.451 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.451 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.451 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 1u0h | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1u0h | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.450 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.450 | |
| 3bt9 | DEQ | HTH-type transcriptional regulator QacR | / | 0.450 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.450 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.450 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.449 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.449 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.448 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.448 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.448 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.448 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.448 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.448 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.447 | |
| 1efz | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.447 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.447 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.447 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 4n4t | 2GV | Tankyrase-1 | 2.4.2.30 | 0.447 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.446 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.446 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.446 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.446 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.446 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.445 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.445 | |
| 2p15 | EZT | Estrogen receptor | / | 0.445 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.445 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.445 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.445 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.445 | |
| 4zas | TYD | CalS13 | / | 0.445 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.445 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.445 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1pj6 | FOL | Dimethylglycine oxidase | 1.5.3.10 | 0.444 | |
| 1zos | MTM | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | / | 0.444 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.444 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.444 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4eh8 | IRG | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 1o1v | TCH | Gastrotropin | / | 0.443 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.443 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.443 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.443 | |
| 4aoi | 4K0 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.443 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 4hkk | AGI | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.443 | |
| 1ppj | ANY | Cytochrome b | / | 0.442 | |
| 2i0y | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.442 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.442 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.442 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.442 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.442 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.441 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.441 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.441 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.441 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.441 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.441 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.441 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.441 | |
| 4eqr | FAD | Coenzyme A disulfide reductase | / | 0.441 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.441 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 1syn | F89 | Thymidylate synthase | / | 0.440 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.440 | |
| 2r5n | TPP | Transketolase 1 | / | 0.440 | |
| 2rtm | IMI | Streptavidin | / | 0.440 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.440 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.440 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.440 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.440 | |
| 3up3 | XCA | aceDAF-12 | / | 0.440 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.440 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.440 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.440 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.440 |