Receptor
PDB id Resolution Class Description Source Keywords
2ZL4 2.5 Å EC: 3.4.21.92 CRYSTAL STRUCTURE OF H.PYLORI CLPP S99A IN COMPLEX WITH THE PEPTIDE AAAA HELICOBACTER PYLORI PEPTIDE SUBSTRATE TETRA-ALA CYTOPLASM HYDROLASE PROTEASE SERINE PROTEASE
Ref.: THE STRUCTURAL BASIS FOR THE ACTIVATION AND PEPTIDE RECOGNITION OF BACTERIAL CLPP J.MOL.BIOL. V. 379 760 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA ALA ALA ALA 1:201;
2:201;
O:201;
P:201;
Q:201;
R:201;
S:201;
T:201;
U:201;
V:201;
W:201;
X:201;
Y:201;
Z:201;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
302.331 n/a O=C([...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZL4 2.5 Å EC: 3.4.21.92 CRYSTAL STRUCTURE OF H.PYLORI CLPP S99A IN COMPLEX WITH THE PEPTIDE AAAA HELICOBACTER PYLORI PEPTIDE SUBSTRATE TETRA-ALA CYTOPLASM HYDROLASE PROTEASE SERINE PROTEASE
Ref.: THE STRUCTURAL BASIS FOR THE ACTIVATION AND PEPTIDE RECOGNITION OF BACTERIAL CLPP J.MOL.BIOL. V. 379 760 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ZL4 - ALA ALA ALA ALA n/a n/a
2 2ZL2 - ASN VAL LEU GLY PHE THR GLN n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3MT6 - OTT PHE SER PRO MAA ALA MP8 n/a n/a
2 3KTI - OTT PHE SER PRO MAA ALA MP8 n/a n/a
3 5DKP - OTT PHE SER PRO MAA ALA MP8 n/a n/a
4 2ZL4 - ALA ALA ALA ALA n/a n/a
5 2ZL2 - ASN VAL LEU GLY PHE THR GLN n/a n/a
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3MT6 - OTT PHE SER PRO MAA ALA MP8 n/a n/a
2 3KTI - OTT PHE SER PRO MAA ALA MP8 n/a n/a
3 5DKP - OTT PHE SER PRO MAA ALA MP8 n/a n/a
4 2ZL4 - ALA ALA ALA ALA n/a n/a
5 2ZL2 - ASN VAL LEU GLY PHE THR GLN n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ALA ALA ALA ALA; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ALA ALA ALA 1 1
2 ALA ALA ALA ALA ALA ALA ALA 1 1
3 ALA ALA ALA ALA ALA ALA 1 1
4 ALA ALA ALA 0.966667 1
5 DAL DAL 0.741935 0.84
6 ALA ALA 0.741935 0.84
7 ALA ALA ALA ALA SER ALA ALA 0.681818 0.694444
8 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.652174 0.806452
9 ALA THR ALA ALA 0.627907 0.833333
10 ALA ALA ALA ALA ALA 0.615385 0.92
11 ASP GLN ILE ILE 0.48 0.833333
12 VAL THR SER VAL VAL 0.444444 0.675676
13 MET VAL GLY GLY VAL VAL ILE ALA 0.44186 0.724138
14 ALA LEU ALA LEU 0.431373 0.806452
15 ALA ILE ALA VAL 0.423077 0.806452
16 ALA ALA SER ALA SER ALA 0.415094 0.648649
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 78
This union binding pocket(no: 1) in the query (biounit: 2zl4.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2TCL RO4 0.003737 0.45268 None
2 2FV5 541 0.008378 0.44186 None
3 1MJH ATP 0.009776 0.42461 None
4 2Q7V FAD 0.04524 0.41117 None
5 4IEN COA 0.02625 0.4002 None
6 2ED4 FAD 0.02163 0.41813 2.01342
7 1XRO LEU 0.006402 0.45506 2.04082
8 1LBT T80 0.02926 0.4034 2.04082
9 3A7R LAQ 0.04232 0.40512 2.55102
10 3PC3 P1T 0.03065 0.40227 2.55102
11 2W14 WR2 0.01959 0.40217 2.55102
12 3FMI KAP 0.008203 0.43013 2.78884
13 3KIF GDL 0.004951 0.42043 2.83019
14 4C2G ALA ALA ALA ALA 0.000000618 0.6255 3.06122
15 3QF7 ANP 0.01295 0.42789 3.06122
16 1WG8 SAM 0.01923 0.41302 3.06122
17 1TL2 NDG 0.006457 0.41298 3.06122
18 1N2X SAM 0.03053 0.40563 3.06122
19 1KMQ GNP 0.03433 0.4005 3.26087
20 3CBG SAH 0.005858 0.43888 3.57143
21 4C2C ALA ALA ALA 0.0005714 0.43572 3.57143
22 2QRK AMP 0.04677 0.40876 3.57143
23 1J5P NAD 0.04127 0.40483 3.57143
24 4JE7 BB2 0.01189 0.42215 4.08163
25 1IUP ALQ 0.02479 0.41997 4.08163
26 1ORR NAD 0.02779 0.41622 4.08163
27 1UMD TDP COI 0.02196 0.41544 4.08163
28 2A92 NAI 0.03044 0.41437 4.08163
29 3BIY 01K 0.02745 0.40836 4.08163
30 4JK3 NAD 0.03605 0.40101 4.08163
31 2J9D ADP 0.02703 0.40014 4.20168
32 1VCO GLN 0.0008722 0.46415 4.59184
33 1LTH NAD 0.01591 0.42062 4.59184
34 1GT6 OLA 0.01144 0.41687 4.59184
35 5O4J SAH 0.04533 0.40208 4.74453
36 5O4J 9KH 0.04533 0.40208 4.74453
37 3O84 HTJ 0.03078 0.40637 5.10204
38 1A8S PPI 0.008421 0.4003 5.10204
39 4MYD 164 0.01066 0.42322 5.61225
40 4OB6 S2T 0.01149 0.41234 5.61225
41 1ME8 RVP 0.04844 0.40544 5.61225
42 3E7W AMP 0.01945 0.40386 5.61225
43 1JUV NDP 0.03919 0.40206 5.69948
44 4L8F MTX 0.001314 0.44968 6.12245
45 4ETZ C2E 0.007319 0.40034 6.12245
46 2NV2 GLN 0.0006711 0.46758 7.14286
47 4GUS FAD 0.01045 0.44906 7.14286
48 4LXH C1E 0.00351 0.4451 7.14286
49 4HSU FAD 0.01413 0.44148 7.14286
50 2G2Y MLI 0.002471 0.40475 7.14286
51 4EYG VNL 0.0176 0.40375 7.14286
52 3PE6 ZYH 0.0136 0.42721 7.65306
53 3T3C 017 0.01474 0.42655 8.08081
54 4WZV E40 0.04288 0.40289 8.125
55 1FIQ SAL 0.02226 0.41851 8.16327
56 1FIQ MTE 0.02025 0.41851 8.16327
57 1V97 MTE 0.0347 0.41575 8.16327
58 2RHW C0E 0.004345 0.4589 8.67347
59 5UAV NDP 0.04164 0.40874 8.67347
60 5UAV TFB 0.04333 0.40874 8.67347
61 1A8U BEZ 0.009196 0.40775 8.67347
62 3QM1 ZYC 0.003358 0.44201 9.69388
63 4I42 1HA 0.0165 0.42206 10.2041
64 4G9E C4L 0.01275 0.41853 10.2041
65 4G4S LDZ 0.0226 0.40307 10.7143
66 1Q0S SAH 0.03033 0.40283 10.7143
67 3R1V AZB 0.00936 0.43196 11.0236
68 4HZD COA 0.005518 0.44168 11.2245
69 1N62 MCN 0.04796 0.40352 11.2245
70 2C0U FAD NBT 0.03556 0.41523 11.7347
71 1ON3 MCA 0.01837 0.41882 12.2449
72 3GD4 FAD 0.04853 0.40542 12.7551
73 1L3I SAH 0.03337 0.40079 13.0208
74 3EXH TPP 0.02974 0.40147 13.2653
75 3HRD MCN 0.03462 0.41231 14.7959
76 4PLG NAI 0.03919 0.4131 16.3265
77 3F8D FAD 0.03631 0.43355 17.3469
78 4B9Q ATP 0.0287 0.40156 19.898
Pocket No.: 2; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 2zl4.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3V2Q PLM 0.03838 0.40371 None
2 1MMQ RRS 0.02105 0.40255 None
3 2PHN GDP 0.03062 0.40235 3.06122
4 1UAY ADN 0.01449 0.40678 3.57143
5 1ZBQ NAD 0.04109 0.4055 3.57143
6 4POO SAM 0.02328 0.41005 4.08163
7 5KKA 6V0 0.03056 0.41249 4.59184
8 4XOE KGM 0.005617 0.41974 6.63265
9 4E5N NAD 0.04752 0.40097 7.14286
10 1GQ2 NAP 0.03263 0.4075 9.69388
11 2Z6J FMN 0.01541 0.4249 11.7347
12 5TDF 7A3 0.02328 0.40032 13.7755
13 1V3S ATP 0.01929 0.40807 13.7931
Pocket No.: 3; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 14
This union binding pocket(no: 3) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BNF UTP 0.03217 0.404 None
2 2ZB3 NDP 0.03929 0.40449 2.55102
3 5AOA PPI 0.01363 0.40331 2.55102
4 1LLF F23 0.04921 0.4063 3.06122
5 1SOW NAD 0.04608 0.40458 3.57143
6 1SC6 NAD 0.04071 0.408 4.08163
7 1LDN NAD 0.04331 0.40439 4.08163
8 3TWO NDP 0.034 0.41449 4.59184
9 1CZI PRO PHI SMC NOR 0.03344 0.40093 5.10204
10 3WV1 WHH 0.02372 0.43101 5.26316
11 3NC9 TR3 0.03355 0.41833 9.69388
12 2GRU NAD 0.02597 0.40942 11.2245
13 1I0Z NAI 0.04378 0.40315 12.2449
14 1BKJ FMN 0.02687 0.41004 13.2653
Pocket No.: 4; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 2zl4.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MFI LYS ARG LYS ARG LYS ARG LYS ARG 0.02971 0.43212 4.08163
2 1YQZ FAD 0.03555 0.4253 5.61225
3 3LZW FAD 0.04906 0.40344 6.63265
Pocket No.: 5; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 7
This union binding pocket(no: 5) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3M6W SAM 0.02339 0.40014 4.59184
2 1HFS L04 0.002211 0.47806 5
3 2CSN CKI 0.02884 0.40811 6.63265
4 4GUT FAD 0.04109 0.41804 7.14286
5 1IHU ADP 0.02521 0.40518 9.18367
6 3S1S SAH 0.02998 0.40493 10.7143
7 3RK0 AMP 0.01584 0.40361 13.2653
Pocket No.: 6; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 10
This union binding pocket(no: 6) in the query (biounit: 2zl4.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CIP ATP 0.03985 0.41568 3.06122
2 5TH5 MET 0.0123 0.40063 4.08163
3 4IZC 1GZ 0.0409 0.40561 5.61225
4 4QIJ 1HA 0.01872 0.45488 6.12245
5 1LYB IVA VAL VAL STA ALA STA 0.02955 0.40857 6.63265
6 1ZVX FIN 0.02044 0.42414 6.74847
7 1NZY BCA 0.02597 0.41157 8.67347
8 1JXZ BCA 0.02775 0.41003 8.67347
9 3WSJ MK1 0.02995 0.41185 10.3448
10 4CIB 7UZ 0.005894 0.40732 11.7347
Pocket No.: 7; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 17
This union binding pocket(no: 7) in the query (biounit: 2zl4.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3HY9 098 0.01576 0.41081 None
2 1BKC INN 0.01198 0.40872 None
3 2XTZ GSP 0.03086 0.40359 1.53061
4 3CAQ NDP 0.04242 0.41332 4.59184
5 1RM8 BAT 0.00857 0.40827 4.73373
6 5W71 9YM 0.0443 0.41141 5.10204
7 2E2R 2OH 0.04018 0.40813 5.10204
8 1R37 NAD 0.03254 0.41314 5.61225
9 1FBL HTA 0.005163 0.42442 6.12245
10 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.03494 0.40823 6.12245
11 2D4V NAD 0.02196 0.41414 7.14286
12 1K7L 544 0.02564 0.40923 8.16327
13 2GU8 796 0.04073 0.42192 9.18367
14 4PNE SAH 0.02728 0.40498 9.18367
15 3NZW BOC TY5 ALA RE0 ABN 0.00905 0.42999 10.2041
16 5CSS G3P 0.01501 0.40152 10.2041
17 1G4U GDP 0.01711 0.40899 11.2245
Pocket No.: 8; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 13
This union binding pocket(no: 8) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1K4M NAD 0.03669 0.40313 2.55102
2 3C3Y SAH 0.03021 0.40056 3.06122
3 1HYH NAD 0.04628 0.40368 4.08163
4 3OJO NAD 0.0313 0.40474 4.59184
5 1T26 NAI 0.0399 0.41761 5.61225
6 4RQU NAD 0.04326 0.40287 5.61225
7 1J49 NAD 0.04576 0.4015 5.61225
8 1YJQ NAP 0.03443 0.41295 6.12245
9 1FFU CDP 0.0415 0.41247 6.74847
10 4FWE FAD 0.04411 0.41391 7.14286
11 2YAK OSV 0.03741 0.40572 9.69388
12 1V8B NAD 0.04986 0.40702 10.7143
13 1UDB NAD 0.04267 0.42155 15.3061
Pocket No.: 9; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 3
This union binding pocket(no: 9) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SSQ CYS 0.03629 0.4075 5.61225
2 1ITZ TPP 0.02949 0.40488 6.63265
3 4MP8 NAD 0.04626 0.40899 11.2245
Pocket No.: 10; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 5
This union binding pocket(no: 10) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5M8T 0TR 0.01176 0.40421 3.57143
2 4R6W SAH 0.04922 0.40038 3.57143
3 3OVR 5SP 0.02775 0.40453 4.08163
4 2E5A LAQ 0.04123 0.40176 5.10204
5 1DFO PLG 0.02724 0.40193 8.63309
Pocket No.: 11; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 31
This union binding pocket(no: 11) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.04318 0.40106 None
2 3G5K BB2 0.02219 0.40106 None
3 2UZH CDP 0.02619 0.40005 2.42424
4 4USQ FAD 0.04949 0.40505 3.06122
5 3VEH 0GA 0.0303 0.40079 3.57143
6 3KPB SAM 0.02197 0.40307 4.09836
7 1YP1 LYS ASN LEU 0.008852 0.40886 4.59184
8 1VPV PLM 0.03841 0.40247 4.59184
9 4AF0 IMP 0.02663 0.40477 5.10204
10 5WDR GNP 0.0187 0.41738 5.26316
11 5W4W 9WG 0.02781 0.40694 5.61225
12 3EYA TDP 0.0178 0.41941 6.12245
13 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.04382 0.40561 6.12245
14 2UZI GTP 0.02352 0.41039 6.62651
15 4GKV NAD 0.03713 0.40989 6.63265
16 2WMO GTP 0.01496 0.40838 6.63265
17 4K81 GTP 0.02476 0.412 7.14286
18 1F76 FMN 0.01163 0.42899 8.16327
19 5EE5 GTP 0.01683 0.41455 8.18713
20 1UPT GTP 0.0274 0.40321 8.18713
21 3NKV GNP 0.02228 0.40804 8.57143
22 4HDQ GNP 0.03087 0.40561 8.98204
23 3GJX GTP 0.03662 0.40169 9.69388
24 1ZCB GDP 0.02674 0.40828 12.7551
25 2JK0 ASP 0.006711 0.40227 13.2653
26 3U4C NDP 0.01835 0.42311 14.7959
27 4HAT GNP 0.03326 0.40569 19.898
28 5UWT GNP 0.03388 0.4039 19.898
29 3M1I GTP 0.03396 0.40386 19.898
30 5UWR GNP 0.0345 0.4034 19.898
31 5UWI GNP 0.03705 0.40165 19.898
Pocket No.: 12; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 13
This union binding pocket(no: 12) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TD3 GLY 0.01222 0.40022 2.43902
2 2Q0L FAD 0.04405 0.41373 2.55102
3 3CX8 GSP 0.03541 0.40571 3.06122
4 1YY5 FAD 0.04117 0.41676 4.59184
5 3KH5 AMP 0.02037 0.4377 5.10204
6 1NVM NAD 0.04917 0.40337 6.08696
7 1BH2 GSP 0.0329 0.40796 6.12245
8 1LFD GNP 0.03619 0.40167 6.12245
9 2VK4 TPP 0.02083 0.41592 9.18367
10 1IHU AF3 0.01549 0.41485 9.18367
11 2F5X ASP 0.01174 0.40176 12.2449
12 2BTO GTP 0.02788 0.40762 12.7551
13 3IAE D7K 0.03715 0.40826 16.3265
Pocket No.: 13; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 3
This union binding pocket(no: 13) in the query (biounit: 2zl4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2RGJ FAD 0.02872 0.41666 4.59184
2 1VI2 NAD 0.03247 0.40075 5.61225
3 1XVB BHL 0.04637 0.40954 5.88235
Pocket No.: 14; Query (leader) PDB : 2ZL4; Ligand: ALA ALA ALA ALA; Similar sites found: 3
This union binding pocket(no: 14) in the query (biounit: 2zl4.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LL5 ATP 0.02572 0.40482 3.57143
2 2X3N FAD 0.03318 0.41566 4.08163
3 9LDT NAD 0.04901 0.40024 11.2245
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