Receptor
PDB id Resolution Class Description Source Keywords
4L8F 1.97 Å EC: 3.4.19.9 CRYSTAL STRUCTURE OF GAMMA-GLUTAMYL HYDROLASE (C108A) COMPLE DANIO RERIO SANDWICHED-LIKE DOMAINS GAMMA-GLUTAMYL HYDROLASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE HYDROLYSIS AND POLYMOR METHOTREXATE POLYGLUTAMATE BY ZEBRAFISH GAMMA-GLUTA HYDROLASE J.MED.CHEM. V. 56 7625 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTX D:301;
B:301;
Valid;
Valid;
none;
none;
submit data
454.439 C20 H22 N8 O5 CN(Cc...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4L8F 1.97 Å EC: 3.4.19.9 CRYSTAL STRUCTURE OF GAMMA-GLUTAMYL HYDROLASE (C108A) COMPLE DANIO RERIO SANDWICHED-LIKE DOMAINS GAMMA-GLUTAMYL HYDROLASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE HYDROLYSIS AND POLYMOR METHOTREXATE POLYGLUTAMATE BY ZEBRAFISH GAMMA-GLUTA HYDROLASE J.MED.CHEM. V. 56 7625 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4L8F - MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 4L8W - MTX DGL DGL n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4L8F - MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 4L8W - MTX DGL DGL n/a n/a
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4L8F - MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 4L8W - MTX DGL DGL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MTX; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 MTX 1 1
2 3BI 0.783505 0.884058
3 2MX 0.778947 0.924242
4 04J 0.663043 0.870968
5 MT1 0.632653 0.968254
6 MOT 0.534653 0.923077
7 COP 0.453782 0.815385
8 FOL 0.410714 0.779412
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4L8F; Ligand: MTX; Similar sites found: 103
This union binding pocket(no: 1) in the query (biounit: 4l8f.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GGU 017 0.01615 0.42135 None
2 2J9D ADP 0.01626 0.41265 None
3 3S43 478 0.02575 0.41038 None
4 3U7S 017 0.02332 0.40894 None
5 2FXD DR7 0.03643 0.40604 None
6 5IDM ANP 0.01077 0.42361 1.11732
7 4GCZ ADP 0.01662 0.41376 1.2987
8 3KL3 GCU 0.00868 0.4021 1.60256
9 3UWV 2PG 0.02543 0.4044 1.91571
10 2VHW NAI 0.006624 0.45273 1.92308
11 4BV6 FAD 0.01635 0.43648 1.92308
12 3WLE NAD 0.0302 0.41833 1.92308
13 2CDU FAD 0.04468 0.40602 1.92308
14 1GUZ NAD 0.04007 0.40394 1.93548
15 3UOY NAP 0.01439 0.45614 2.24359
16 2VVM FAD 0.009469 0.45193 2.24359
17 1V59 FAD 0.02897 0.42067 2.24359
18 2BRY FAD 0.02455 0.41771 2.24359
19 1LDN NAD 0.02783 0.4152 2.24359
20 1RYI FAD 0.04191 0.41189 2.24359
21 1V59 NAD 0.01175 0.40916 2.24359
22 4USR FAD 0.04086 0.40847 2.24359
23 1MV8 NAD 0.03117 0.40371 2.24359
24 3HQP FDP 0.01609 0.40293 2.24359
25 1RP0 AHZ 0.008623 0.44139 2.46479
26 2V3A FAD 0.03472 0.41545 2.5641
27 1X87 NAD 0.02328 0.40938 2.5641
28 1GKZ ADP 0.02344 0.40428 2.5641
29 1FQ5 0GM 0.04111 0.40347 2.5641
30 2EV9 NAP 0.02068 0.4216 2.6616
31 1V8B NAD 0.01314 0.43906 2.88462
32 4CZG ADP 0.01331 0.43832 2.88462
33 2DKH FAD 0.0266 0.41591 2.88462
34 2DKH 3HB 0.03367 0.41591 2.88462
35 4IZC 1GZ 0.03421 0.41259 2.90909
36 4J4H 1J1 0.01876 0.43584 3.0888
37 4J4H NAI 0.01876 0.43584 3.0888
38 4JK3 NAD 0.01019 0.43234 3.0888
39 3G6N MET ALA SER 0.004087 0.40396 3.14136
40 3LAD FAD 0.02591 0.42159 3.20513
41 4JNE ATP 0.02492 0.40928 3.20513
42 2DFV NAD 0.03674 0.40606 3.20513
43 1ZEM NAD 0.02831 0.40761 3.43511
44 4C2G ALA ALA ALA ALA 0.000523 0.48015 3.52564
45 1REO FAD 0.004444 0.46704 3.52564
46 3NJ4 NAD 0.03693 0.45038 3.52564
47 3NJ4 AFX 0.03693 0.45038 3.52564
48 1JQI FAD 0.03046 0.41693 3.52564
49 2GVC FAD 0.004953 0.45571 3.84615
50 5BUK FAD 0.02505 0.42538 3.84615
51 5TDF 7A3 0.009063 0.4238 3.84615
52 2ZKJ ADP 0.04935 0.40939 3.84615
53 2PT9 2MH 0.0458 0.40508 3.84615
54 2PT9 S4M 0.03616 0.40212 3.84615
55 1TLL FMN 0.03411 0.40171 3.84615
56 3KA2 2NC 0.04326 0.41508 3.94089
57 4NTC FAD 0.03622 0.4159 4.16667
58 1SAY PYR 0.03569 0.40677 4.16667
59 1L3I SAH 0.02547 0.40977 4.6875
60 2YVF FAD 0.02128 0.44096 4.80769
61 2YVF NAD 0.02179 0.44096 4.80769
62 2YYY NAP 0.0216 0.41791 4.80769
63 5FJN BE2 0.04048 0.41318 5.12821
64 5FJN FAD 0.03686 0.41318 5.12821
65 3QFU ADP 0.0192 0.40657 5.12821
66 1H82 GZZ 0.01515 0.45345 5.76923
67 1H82 FAD 0.01404 0.45345 5.76923
68 3L9W AMP 0.01028 0.43969 5.76923
69 1DXY NAD 0.02179 0.41006 5.76923
70 3L9W GSH 0.04398 0.40018 5.76923
71 2NV2 GLN 0.0001765 0.49462 5.88235
72 1MO9 FAD 0.02279 0.44593 6.08974
73 1YY5 FAD 0.01809 0.43799 6.08974
74 1ZGD NAP 0.03189 0.41361 6.08974
75 2ZL4 ALA ALA ALA ALA 0.001314 0.44968 6.12245
76 4CNK FAD 0.02628 0.42098 6.41026
77 1I8T FAD 0.03746 0.41522 6.41026
78 2RAB NAD 0.02589 0.43707 6.73077
79 2RAB FAD 0.01557 0.43707 6.73077
80 2B9W FAD 0.03959 0.42413 6.73077
81 2F5Z FAD 0.02786 0.4225 6.73077
82 2ZJ3 G6P 0.01221 0.41897 6.93333
83 1RSG FAD 0.01331 0.44297 7.05128
84 1QO8 FAD 0.02674 0.42108 7.05128
85 4USQ FAD 0.02886 0.41381 7.05128
86 3AD8 NAD 0.007631 0.44574 7.07071
87 3M6P BB2 0.01276 0.41832 7.25389
88 4FWE FAD 0.01172 0.44858 7.37179
89 4XFR CIT 0.002499 0.43379 7.37179
90 2GAG NAD 0.00689 0.45215 7.61905
91 1VCO GLN 0.000000005331 0.65823 7.69231
92 1GET NAP 0.02921 0.43613 7.69231
93 1GET FAD 0.028 0.43613 7.69231
94 1MOQ GLP 0.01485 0.41454 8.01282
95 2E5V FAD 0.02669 0.42453 8.65385
96 3A0T ADP 0.01175 0.42423 9.21053
97 3ICT FAD 0.04141 0.40988 11.2179
98 4NMC FAD 0.03125 0.41707 12.5
99 4NMC 2OP 0.03007 0.41707 12.5
100 1H8P PC 0.004916 0.42283 16.5138
101 1GPM CIT 0.005961 0.40533 17.6282
102 2D37 NAD 0.0465 0.40054 19.8864
103 2D37 FMN 0.04422 0.40054 19.8864
Pocket No.: 2; Query (leader) PDB : 4L8F; Ligand: MTX; Similar sites found: 20
This union binding pocket(no: 2) in the query (biounit: 4l8f.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1CF2 NAP 0.02231 0.41098 1.92308
2 9LDT NAD 0.04236 0.40188 1.92308
3 1KOJ PAN 0.01981 0.40899 2.24359
4 2PZM UDP 0.02051 0.43269 2.5641
5 2PZM NAD 0.02051 0.43269 2.5641
6 4PIV NDP 0.04912 0.40114 2.5641
7 1FL2 FAD 0.02115 0.4272 3.22581
8 4G9E C4L 0.02296 0.40167 3.22581
9 4UP4 NDG 0.01379 0.40858 4.48718
10 2DTX BMA 0.04896 0.40621 4.54545
11 2XVE FAD 0.01162 0.45677 4.80769
12 1MO9 KPC 0.02138 0.44982 6.08974
13 1J0X NAD 0.04712 0.40807 6.08974
14 4L8V NAP 0.04459 0.40019 6.41026
15 3FJO FMN 0.02338 0.40346 7.05128
16 3UCL FAD 0.02605 0.43727 7.37179
17 3UCL CYH 0.02605 0.43727 7.37179
18 3UCL NAP 0.04937 0.42277 7.37179
19 5A0R ACE GLU VAL ASN PRO 0.04667 0.40051 8.08081
20 2FZW NAD 0.0335 0.41776 12.0643
Pocket No.: 3; Query (leader) PDB : 4L8F; Ligand: MTX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4l8f.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4L8F; Ligand: MTX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4l8f.bio3) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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