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 |
|---|---|---|---|
| 2zdv | 37U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.873 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.855 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.829 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.816 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.809 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.789 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.789 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.788 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.781 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.772 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.771 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.759 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.758 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.755 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.751 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.743 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.742 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.739 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.724 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.723 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.722 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.710 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.694 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.693 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.687 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.686 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.685 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.684 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.680 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.675 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.675 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.667 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.665 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.664 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.660 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.659 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.658 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.658 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.658 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.656 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.650 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.647 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.646 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.646 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.644 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.644 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.643 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.640 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.640 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.639 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.638 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.638 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.637 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.637 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.637 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.636 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.636 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.634 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.633 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.627 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.626 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.624 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.622 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.619 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.617 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.615 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.609 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.609 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.608 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.607 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.606 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.604 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.604 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.602 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.602 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.597 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.595 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.594 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.594 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.593 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.592 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.591 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.590 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.587 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.586 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.580 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.575 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.568 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.567 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.565 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.559 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.558 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.557 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.557 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.556 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.554 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.550 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.545 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.541 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.539 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.534 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.532 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.529 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.528 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.519 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.514 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.508 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.507 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.506 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.498 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.491 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.484 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.479 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.470 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.469 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.468 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.466 | |
| 1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.464 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.464 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.463 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.463 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.462 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.462 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.462 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.461 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.461 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.460 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.460 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.458 | |
| 3eks | CY9 | Actin-5C | / | 0.457 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.457 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.457 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.456 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.456 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.455 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.455 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.453 | |
| 1fml | RTL | Retinol dehydratase | / | 0.452 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.452 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.452 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.451 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.450 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.449 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.449 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.448 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.448 | |
| 3eku | CY9 | Actin-5C | / | 0.448 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.448 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.448 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.448 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.447 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.447 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.446 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.446 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.445 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.445 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.444 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.444 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 1ohh | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1ohh | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.443 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.443 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.442 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.442 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.442 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.442 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.442 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.442 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.442 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.441 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.441 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.441 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.441 | |
| 1n95 | FTH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.440 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.440 | |
| 4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 |