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 |
---|---|---|---|
3biv | 11U | Prothrombin | 3.4.21.5 |
PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
---|---|---|---|---|---|
3biv | 11U | Prothrombin | 3.4.21.5 | 1.000 | |
2znk | 31U | Prothrombin | 3.4.21.5 | 0.865 | |
2zdv | 37U | Prothrombin | 3.4.21.5 | 0.846 | |
2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.825 | |
2zda | 32U | Prothrombin | 3.4.21.5 | 0.817 | |
2zgx | 29U | Prothrombin | 3.4.21.5 | 0.807 | |
3biu | 10U | Prothrombin | 3.4.21.5 | 0.792 | |
2ziq | 26U | Prothrombin | 3.4.21.5 | 0.778 | |
2zfq | 45U | Prothrombin | 3.4.21.5 | 0.777 | |
2zff | 53U | Prothrombin | 3.4.21.5 | 0.772 | |
2zhf | 49U | Prothrombin | 3.4.21.5 | 0.765 | |
2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.759 | |
2zfr | 46U | Prothrombin | 3.4.21.5 | 0.752 | |
2zhe | 13U | Prothrombin | 3.4.21.5 | 0.752 | |
7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.737 | |
4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.725 | |
3dhk | 23U | Prothrombin | 3.4.21.5 | 0.723 | |
3dux | 64U | Prothrombin | 3.4.21.5 | 0.710 | |
3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.706 | |
2zhq | 27U | Prothrombin | 3.4.21.5 | 0.703 | |
4bam | MM9 | Prothrombin | 3.4.21.5 | 0.702 | |
2zgb | 21U | Prothrombin | 3.4.21.5 | 0.692 | |
2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.669 | |
1mue | CDD | Prothrombin | 3.4.21.5 | 0.666 | |
3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.664 | |
2zfp | 19U | Prothrombin | 3.4.21.5 | 0.655 | |
1zrb | 062 | Prothrombin | 3.4.21.5 | 0.653 | |
1d6w | 00R | Prothrombin | 3.4.21.5 | 0.650 | |
1ypg | UIR | Prothrombin | 3.4.21.5 | 0.649 | |
4bak | M67 | Prothrombin | 3.4.21.5 | 0.645 | |
2r2m | I50 | Prothrombin | 3.4.21.5 | 0.643 | |
3f68 | 91U | Prothrombin | 3.4.21.5 | 0.641 | |
1ypk | CCR | Prothrombin | 3.4.21.5 | 0.638 | |
1afe | ALZ | Prothrombin | 3.4.21.5 | 0.628 | |
1k21 | IGN | Prothrombin | 3.4.21.5 | 0.628 | |
1t4v | 14A | Prothrombin | 3.4.21.5 | 0.628 | |
1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.627 | |
2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.627 | |
3egk | M18 | Prothrombin | 3.4.21.5 | 0.627 | |
2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.625 | |
1d4p | BPP | Prothrombin | 3.4.21.5 | 0.624 | |
1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.621 | |
1o0d | 163 | Prothrombin | 3.4.21.5 | 0.620 | |
1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.618 | |
3qwc | 98P | Prothrombin | 3.4.21.5 | 0.617 | |
1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.615 | |
1z71 | L17 | Prothrombin | 3.4.21.5 | 0.615 | |
3c1k | T15 | Prothrombin | 3.4.21.5 | 0.615 | |
2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.611 | |
1ypj | UIB | Prothrombin | 3.4.21.5 | 0.608 | |
1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.605 | |
1d3d | BZT | Prothrombin | 3.4.21.5 | 0.604 | |
2v3o | I26 | Prothrombin | 3.4.21.5 | 0.604 | |
1bcu | PRL | Prothrombin | 3.4.21.5 | 0.603 | |
1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.599 | |
1c5n | ESI | Prothrombin | 3.4.21.5 | 0.599 | |
1ype | UIP | Prothrombin | 3.4.21.5 | 0.599 | |
3qto | 10P | Prothrombin | 3.4.21.5 | 0.599 | |
4ban | M6S | Prothrombin | 3.4.21.5 | 0.598 | |
4baq | M4Z | Prothrombin | 3.4.21.5 | 0.595 | |
3p17 | 99P | Prothrombin | 3.4.21.5 | 0.590 | |
1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.589 | |
1vzq | SHY | Prothrombin | 3.4.21.5 | 0.585 | |
3c27 | DKK | Prothrombin | 3.4.21.5 | 0.584 | |
1ghv | 120 | Prothrombin | 3.4.21.5 | 0.582 | |
1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.581 | |
1jwt | BLI | Prothrombin | 3.4.21.5 | 0.580 | |
4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.578 | |
1d9i | 00P | Prothrombin | 3.4.21.5 | 0.573 | |
2uuk | 897 | Prothrombin | 3.4.21.5 | 0.571 | |
4bah | MEL | Prothrombin | 3.4.21.5 | 0.568 | |
2gde | SN3 | Prothrombin | 3.4.21.5 | 0.567 | |
1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.566 | |
4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.566 | |
2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.561 | |
2bdy | UNB | Prothrombin | 3.4.21.5 | 0.560 | |
1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.559 | |
2uuj | 896 | Prothrombin | 3.4.21.5 | 0.558 | |
2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.557 | |
2pks | G44 | Prothrombin | 3.4.21.5 | 0.556 | |
1nzq | 162 | Prothrombin | 3.4.21.5 | 0.554 | |
2v3h | I25 | Prothrombin | 3.4.21.5 | 0.554 | |
3qtv | 06P | Prothrombin | 3.4.21.5 | 0.554 | |
1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.552 | |
4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.550 | |
4bao | MVF | Prothrombin | 3.4.21.5 | 0.549 | |
1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.548 | |
1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.547 | |
1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.546 | |
1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.543 | |
4loy | 6XS | Prothrombin | 3.4.21.5 | 0.543 | |
2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.536 | |
4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.536 | |
2bxt | C2D | Prothrombin | 3.4.21.5 | 0.533 | |
1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.526 | |
1o2g | 696 | Prothrombin | 3.4.21.5 | 0.523 | |
1k22 | MEL | Prothrombin | 3.4.21.5 | 0.521 | |
1uma | IN2 | Prothrombin | 3.4.21.5 | 0.521 | |
2zhw | 12U | Prothrombin | 3.4.21.5 | 0.518 | |
4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.518 | |
1w7g | MIU | Prothrombin | 3.4.21.5 | 0.504 | |
4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.504 | |
1c1u | BAI | Prothrombin | 3.4.21.5 | 0.500 | |
1riw | OSC | Prothrombin | 3.4.21.5 | 0.499 | |
4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.499 | |
1oyt | FSN | Prothrombin | 3.4.21.5 | 0.484 | |
3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.484 | |
4fuf | 8UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.480 | |
2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.478 | |
1wqv | PSM | Coagulation factor VII | 3.4.21.21 | 0.477 | |
2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.477 | |
4fuj | 1U9 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.474 | |
4kgk | GTP | Uncharacterized protein | / | 0.474 | |
2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.473 | |
5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.473 | |
2zp0 | PI0 | Coagulation factor VII | 3.4.21.21 | 0.469 | |
4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.468 | |
4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.468 | |
1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.467 | |
1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.466 | |
2nr4 | FMN | Conserved protein | / | 0.466 | |
3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.465 | |
3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.463 | |
4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.463 | |
1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.462 | |
2e1m | FAD | L-glutamate oxidase | / | 0.462 | |
2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.462 | |
2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.461 | |
3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.461 | |
4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.461 | |
1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.460 | |
1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.460 | |
2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.460 | |
4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.460 | |
4q71 | FAD | Bifunctional protein PutA | / | 0.459 | |
1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.457 | |
2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.457 | |
2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.457 | |
1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.456 | |
2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.456 | |
2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.456 | |
2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.456 | |
2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.456 | |
4uth | FMN | Xenobiotic reductase | / | 0.456 | |
1j1z | ATP | Argininosuccinate synthase | / | 0.455 | |
1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.455 | |
1tyt | FAD | Trypanothione reductase | 1.8.1.12 | 0.455 | |
2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.455 | |
4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.455 | |
2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.454 | |
3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.454 | |
4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.454 | |
3vil | SA0 | Beta-glucosidase | / | 0.453 | |
4d03 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
4fui | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.453 | |
4kby | C2E | Stimulator of interferon genes protein | / | 0.453 | |
4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.453 | |
1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
2ejz | SAH | Diphthine synthase | / | 0.452 | |
2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.452 | |
3pft | FMN | Flavin reductase | / | 0.452 | |
3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.452 | |
4lzw | THM | Uridine phosphorylase | / | 0.452 | |
1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.451 | |
2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.450 | |
2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.450 | |
3ai0 | PNW | Beta-glucosidase | / | 0.450 | |
4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.450 | |
4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.450 | |
4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.450 | |
2jk6 | FAD | Trypanothione reductase | / | 0.449 | |
2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
2y5h | Y5H | Coagulation factor X | 3.4.21.6 | 0.449 | |
3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
3po6 | DT9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.448 | |
2g1n | 1IG | Renin | 3.4.23.15 | 0.448 | |
2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.448 | |
3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.448 | |
3fp0 | FP0 | 15-O-acetyltransferase | / | 0.448 | |
3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.448 | |
3swc | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.448 | |
4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.448 | |
4fub | 4UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.448 | |
5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.448 | |
1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.447 | |
2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.447 | |
4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.447 | |
4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.447 | |
1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.446 | |
2g00 | 4QC | Coagulation factor X | 3.4.21.6 | 0.446 | |
3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.446 | |
3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.446 | |
3i7v | B4P | AP4A hydrolase | / | 0.446 | |
3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.446 | |
3zei | AWH | O-acetylserine sulfhydrylase | / | 0.446 | |
2c4f | GIL | Coagulation factor VII | 3.4.21.21 | 0.445 | |
4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.445 | |
1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
1fec | FAD | Trypanothione reductase | 1.8.1.12 | 0.444 | |
1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.444 | |
1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.444 | |
2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.443 | |
1owk | 303 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.443 | |
1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
2b9y | FAD | Putative aminooxidase | / | 0.443 | |
2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.443 | |
2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.443 | |
4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
4m5p | FMN | NADPH dehydrogenase | / | 0.443 | |
2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.442 | |
2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.442 | |
3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
3v4a | PK1 | Androgen receptor | / | 0.442 | |
3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.442 | |
1fml | RTL | Retinol dehydratase | / | 0.441 | |
1okl | MNS | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.441 | |
2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
2fe4 | GDP | Ras-related protein Rab-6B | / | 0.441 | |
2iej | S48 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.441 | |
4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.441 | |
4yfy | 0FX | VioF | / | 0.441 | |
1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
1khe | GCP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.440 | |
2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.440 | |
2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
2v16 | C47 | Renin | 3.4.23.15 | 0.440 | |
2x8h | FAD | Thioredoxin glutathione reductase | / | 0.440 | |
2ywl | FAD | Thioredoxin reductase related protein | / | 0.440 | |
3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.440 | |
3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.440 | |
3e8x | NAP | BH1520 protein | / | 0.440 | |
3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.440 | |
4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.440 | |
5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 |