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 |
---|---|---|---|
1brp | RTL | Retinol-binding protein 4 |
PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
---|---|---|---|---|---|
1brp | RTL | Retinol-binding protein 4 | / | 1.000 | |
1iiu | RTL | Retinol-binding protein 4 | / | 0.645 | |
1kt7 | RTL | Retinol-binding protein 4 | / | 0.630 | |
1aqb | RTL | Retinol-binding protein 4 | / | 0.627 | |
1fel | FEN | Retinol-binding protein 4 | / | 0.622 | |
1kt3 | RTL | Retinol-binding protein 4 | / | 0.621 | |
1kt4 | RTL | Retinol-binding protein 4 | / | 0.616 | |
1kt6 | RTL | Retinol-binding protein 4 | / | 0.610 | |
3fmz | 2T1 | Retinol-binding protein 4 | / | 0.535 | |
4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.488 | |
3tox | NAP | Putative oxidoreductase | / | 0.486 | |
4iui | 1GQ | Estrogen receptor | / | 0.478 | |
2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.475 | |
4j6c | STR | Cytochrome P450 monooxygenase | / | 0.474 | |
2won | ZZE | Gag-Pol polyprotein | 2.7.7.49 | 0.473 | |
5fm7 | ADP | RuvB-like helicase | / | 0.472 | |
1ot7 | CHC | Bile acid receptor | / | 0.470 | |
3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
5jtb | ZMA | Adenosine receptor A2a | / | 0.469 | |
1thn | ADP | Anti-sigma F factor | / | 0.467 | |
3bfa | 9OD | Odorant binding protein ASP1 | / | 0.467 | |
4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.467 | |
4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.467 | |
1tvr | TB9 | Gag-Pol polyprotein | 2.7.7.49 | 0.465 | |
1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.465 | |
3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.465 | |
4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.465 | |
5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.465 | |
2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
3ang | DCC | Transcriptional repressor, TetR family | / | 0.464 | |
5ecc | NAP | Dehydrofolate reductase type I | / | 0.464 | |
1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.463 | |
1upw | 444 | Oxysterols receptor LXR-beta | / | 0.463 | |
2ayl | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.463 | |
3dlg | GWE | Gag-Pol polyprotein | 2.7.7.49 | 0.463 | |
3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.463 | |
4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.463 | |
4lb2 | DM5 | Serum albumin | / | 0.463 | |
1fcx | 184 | Retinoic acid receptor gamma | / | 0.462 | |
1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.462 | |
2fon | FAD | Acyl-coenzyme A oxidase | / | 0.462 | |
3ipt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.462 | |
3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
4h4o | 506 | Gag-Pol polyprotein | 2.7.7.49 | 0.462 | |
1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.460 | |
2xvv | 9DN | Serum albumin | / | 0.460 | |
3ict | ADP | Coenzyme A disulfide reductase | / | 0.460 | |
3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.459 | |
1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.458 | |
1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
3w5p | 4OA | Vitamin D3 receptor | / | 0.458 | |
4hyf | 1AK | Tankyrase-2 | 2.4.2.30 | 0.458 | |
4pd6 | URI | Nucleoside permease | / | 0.458 | |
5k2d | ZMA | Adenosine receptor A2a | / | 0.458 | |
1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
2y5d | NAP | 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase | / | 0.457 | |
3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.457 | |
3u8h | BHP | Phospholipase A2, membrane associated | / | 0.457 | |
5ikr | ID8 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.457 | |
2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.456 | |
2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.456 | |
3gwf | FAD | Cyclohexanone monooxygenase | / | 0.456 | |
3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.456 | |
3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.456 | |
3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.456 | |
4l8u | 9AZ | Serum albumin | / | 0.456 | |
5k2b | ZMA | Adenosine receptor A2a | / | 0.456 | |
1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.455 | |
2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.455 | |
2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.455 | |
3a1l | 2CC | Cytochrome P450 | / | 0.455 | |
3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.455 | |
3c6t | M14 | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
3vt7 | VDX | Vitamin D3 receptor | / | 0.455 | |
3vtd | TKD | Vitamin D3 receptor | / | 0.455 | |
4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.455 | |
4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.455 | |
1osv | CHC | Bile acid receptor | / | 0.454 | |
1rd4 | L08 | Integrin alpha-L | / | 0.454 | |
1xdk | REA | Retinoic acid receptor beta | / | 0.454 | |
2be2 | R22 | Gag-Pol polyprotein | 2.7.7.49 | 0.454 | |
2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.454 | |
2ydv | NEC | Adenosine receptor A2a | / | 0.454 | |
3c3e | GDP | 2-phospho-L-lactate transferase | / | 0.454 | |
3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
3lal | KRV | Gag-Pol polyprotein | 2.7.7.49 | 0.454 | |
3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.454 | |
3vt5 | YI2 | Vitamin D3 receptor | / | 0.454 | |
4eoi | 1RO | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.454 | |
1qnf | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.453 | |
2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.453 | |
4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.453 | |
5k2a | ZMA | Adenosine receptor A2a | / | 0.453 | |
1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
2y05 | NAP | Prostaglandin reductase 1 | / | 0.452 | |
1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
2b1i | 93A | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.451 | |
2hnz | PC0 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.451 | |
3eq6 | BCO | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.451 | |
3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
1al7 | HST | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.450 | |
1fd0 | 254 | Retinoic acid receptor gamma | / | 0.450 | |
1kt5 | RTL | Retinol-binding protein 4 | / | 0.450 | |
3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.449 | |
2z78 | H86 | Geranylgeranyl pyrophosphate synthase | / | 0.449 | |
3bzu | A21 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
3t1a | 5MA | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
3tm5 | SFG | Uncharacterized protein | / | 0.449 | |
2wd8 | VGF | Pteridine reductase | / | 0.448 | |
2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.448 | |
3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.448 | |
4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.448 | |
3eml | ZMA | Adenosine receptor A2a | / | 0.448 | |
1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
1jq5 | NAD | Glycerol dehydrogenase | 1.1.1.6 | 0.447 | |
1m52 | P17 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.447 | |
2r0p | K2C | Putative FAD-monooxygenase | / | 0.447 | |
3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
3drp | R8E | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
3w0h | W12 | Vitamin D3 receptor | / | 0.447 | |
4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.447 | |
4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
5k2c | ZMA | Adenosine receptor A2a | / | 0.447 | |
1lri | CLR | Beta-elicitin cryptogein | / | 0.446 | |
1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.446 | |
1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
1xdd | AAY | Integrin alpha-L | / | 0.446 | |
2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.446 | |
3mg3 | ECH | Orange carotenoid-binding protein | / | 0.446 | |
3nwl | NDP | Catalase | 1.11.1.6 | 0.446 | |
3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.446 | |
4fm5 | DF0 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
1c7o | PPG | Hemolysin | / | 0.445 | |
2ydo | ADN | Adenosine receptor A2a | / | 0.445 | |
2ykb | YKB | Heat shock protein HSP 90-alpha | / | 0.445 | |
3gkj | HC3 | Niemann-Pick C1 protein | / | 0.445 | |
3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
4a32 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
4a51 | DQ8 | Kinesin-like protein KIF11 | / | 0.445 | |
4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.445 | |
4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
1r2j | FAD | FkbI | / | 0.444 | |
1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
1til | ATP | Anti-sigma F factor | / | 0.444 | |
2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
2ylt | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.444 | |
3eej | 53R | Uncharacterized protein | / | 0.444 | |
3lam | KRP | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
3zei | AWH | O-acetylserine sulfhydrylase | / | 0.444 | |
4ejn | 0R4 | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.444 | |
5iua | 6DX | Adenosine receptor A2a | / | 0.444 | |
4ug2 | NGI | Adenosine receptor A2a | / | 0.444 | |
1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
1dv2 | ATP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
1td2 | PXL | Pyridoxal kinase PdxY | / | 0.443 | |
1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.443 | |
1w22 | NHB | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
2zyn | BCD | Periplasmic binding protein | / | 0.443 | |
3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.443 | |
3znq | SS8 | D-amino-acid oxidase | 1.4.3.3 | 0.443 | |
4eiy | ZMA | Adenosine receptor A2a | / | 0.443 | |
4h4m | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
5dg3 | U21 | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | / | 0.443 | |
1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
1skg | VAL_ALA_PHE_ARG_SER | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.442 | |
2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.442 | |
2lf1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
2ynf | WHU | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
3new | 3NE | Mitogen-activated protein kinase 14 | / | 0.442 | |
3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
3q71 | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.442 | |
4fiz | CUE | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
4hxy | NDP | Plm1 | / | 0.442 | |
4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.442 | |
1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.441 | |
3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
5a3c | NAD | SIR2 family protein | / | 0.441 | |
1dgb | NDP | Catalase | 1.11.1.6 | 0.440 | |
1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.440 | |
2ban | 357 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
2fto | CB3 | Thymidylate synthase | / | 0.440 | |
3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
4ia2 | BIV | Vitamin D3 receptor A | / | 0.440 | |
4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
4rup | H97 | Vitamin D3 receptor A | / | 0.440 |