Receptor
PDB id Resolution Class Description Source Keywords
5FQJ 2.27 Å EC: 3.5.2.6 W229D MUTANT OF THE LAST COMMON ANCESTOR OF GRAM-NEGATIVE BA (GNCA) BETA-LACTAMASE BOUND TO 5(6)-NITROBENZOTRIAZOLE (TS- SYNTHETIC CONSTRUCT HYDROLASE PRECAMBRIAN RESURRECTED BETA-LACTAMASE GNCA
Ref.: DE NOVO ACTIVE SITES FOR RESURRECTED PRECAMBRIAN EN NAT COMMUN V. 8 16113 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6NT A:1295;
Valid;
none;
submit data
164.122 C6 H4 N4 O2 c1cc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FQK 1.77 Å EC: 3.5.2.6 W229D AND F290W MUTANT OF THE LAST COMMON ANCESTOR OF GRAM-N BACTERIA (GNCA4) BETA-LACTAMASE CLASS A BOUND TO 5(6)- N ITROBENZOTRIAZOLE (TS-ANALOG) SYNTHETIC CONSTRUCT HYDROLASE PRECAMBRIAN RESURRECTED BETA-LACTAMASE GNCA4
Ref.: DE NOVO ACTIVE SITES FOR RESURRECTED PRECAMBRIAN EN NAT COMMUN V. 8 16113 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
2 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
2 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
4 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
5 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
6 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
7 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
8 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
9 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
10 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
11 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
12 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
13 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
14 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
15 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
16 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
17 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
18 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
19 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
20 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
21 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
22 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
23 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
24 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
25 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
26 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
27 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
28 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
29 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
30 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
31 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
32 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6NT; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6NT 1 1
2 3NY 0.5 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FQK; Ligand: 6NT; Similar sites found: 146
This union binding pocket(no: 1) in the query (biounit: 5fqk.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2D6M LBT 0.001189 0.44578 None
2 1MID LAP 0.00699 0.42037 None
3 4JH6 FCN 0.01362 0.40352 None
4 1W8S FBP 0.009879 0.41692 1.14068
5 4P7X YCP 0.02142 0.40265 1.48699
6 4P7X AKG 0.02142 0.40265 1.48699
7 1VPV PLM 0.01289 0.42763 1.85874
8 3V4S ATP 0.01391 0.41935 1.85874
9 5H2D ERG 0.01962 0.41221 1.85874
10 3FYS PLM 0.02335 0.40898 1.85874
11 5IGI ZIT 0.04968 0.40591 1.85874
12 5IGI GMP 0.04777 0.40591 1.85874
13 4DHY S41 0.03893 0.40109 1.85874
14 5J75 6GQ 0.01766 0.40662 1.89394
15 5JSP DQY 0.002841 0.43196 1.99005
16 2XFH CL6 0.01221 0.43201 2.23048
17 2HFN FMN 0.01924 0.40534 2.23048
18 2X5W K2B 0.03428 0.40408 2.23048
19 4TWL ASC 0.01078 0.40464 2.43902
20 3SAO NKN 0.01487 0.40445 2.5
21 3QCP FAD 0.00923 0.43578 2.60223
22 1PS9 FAD 0.02957 0.42235 2.60223
23 1ODM ASV 0.01583 0.42087 2.60223
24 3OV6 MK0 0.02231 0.41906 2.60223
25 3ICS COA 0.0286 0.41408 2.60223
26 3OZV ECN 0.01273 0.41332 2.60223
27 5MBC FMN 0.01334 0.41123 2.60223
28 4E1O PLP PVH 0.02359 0.40612 2.60223
29 3AVS OGA 0.01372 0.40211 2.60223
30 4XB4 45D 0.0337 0.4091 2.63158
31 3KP6 SAL 0.006205 0.41655 2.64901
32 4N7C AEF 0.009686 0.40126 2.84091
33 3WUC GLC GAL 0.02426 0.40467 2.91971
34 1ZHX HC3 0.005652 0.44641 2.97398
35 1GQG DCD 0.004557 0.44517 2.97398
36 3A7R LAQ 0.02207 0.4243 2.97398
37 5FBN 5WF 0.02279 0.42238 2.97398
38 4YZC STU 0.02808 0.41849 2.97398
39 1M13 HYF 0.03245 0.41135 2.97398
40 4IA6 EIC 0.005448 0.40662 2.97398
41 3ML5 AZM 0.009847 0.40467 2.97398
42 4E5N NAD 0.04517 0.40372 2.97398
43 5APK 76E 0.03009 0.40945 3.01887
44 5NTW 98N 0.04058 0.40416 3.11284
45 2JIG PD2 0.001519 0.42442 3.125
46 2PVN P63 0.02423 0.41363 3.125
47 3MTX PGT 0.03539 0.41019 3.31126
48 5KJZ PCG 0.01531 0.40956 3.33333
49 2GJ5 VD3 0.02489 0.4218 3.34572
50 3ETH ATP 0.01666 0.4147 3.34572
51 1RQJ RIS 0.03373 0.40324 3.34572
52 5C1M 4VO 0.01791 0.40313 3.34572
53 1QY1 PRZ 0.02671 0.40315 3.44828
54 4ZOM 4Q3 0.04621 0.42988 3.55556
55 5N18 8HZ 0.007259 0.41279 3.66972
56 3WVS RRM 0.01015 0.42693 3.71747
57 2PUL ACP 0.01349 0.41132 3.71747
58 2P3I MNA 0.009466 0.41115 3.72671
59 1ND2 MYR 0.008066 0.42115 3.78151
60 4Q0L V14 0.01029 0.43217 3.80228
61 4WW7 AMP 0.00504 0.44157 3.83142
62 5B4B LP5 0.02648 0.4147 4.03226
63 3TO7 COA 0.02405 0.41135 4.08922
64 5NJI 8Z2 0.03099 0.40763 4.08922
65 1ZB6 GST 0.04307 0.4023 4.08922
66 1D1G NDP 0.01019 0.42973 4.16667
67 4X5S AZM 0.008971 0.40509 4.31034
68 3JRS A8S 0.01236 0.41369 4.32692
69 3FS1 MYR 0.01671 0.40747 4.34783
70 1UVC STE 0.02285 0.41492 4.3956
71 4MNS 2AX 0.03993 0.41945 4.40252
72 3KDJ A8S 0.01246 0.41905 4.45545
73 2V58 LZJ 0.02027 0.43363 4.46097
74 3NTD COA 0.02361 0.42201 4.46097
75 3K5I ADP 0.02025 0.4073 4.46097
76 4H6Q TFB 0.0401 0.4037 4.46097
77 4DE9 VTP 0.04503 0.40196 4.46097
78 5LJ0 6XX 0.03302 0.4039 4.61538
79 1Y0G 8PP 0.01606 0.43835 4.71204
80 5UI2 EQ3 0.01818 0.42728 4.83271
81 3NRR D16 0.02881 0.42641 4.83271
82 2P1C GG3 0.02222 0.41789 4.83271
83 5EY0 GTP 0.009036 0.41527 4.83271
84 4K55 H6P 0.003785 0.41782 4.83871
85 5KEW 6SB 0.0003958 0.4746 4.86111
86 5ECP ATP 0.04848 0.41091 4.93274
87 5DXT 5H5 0.01539 0.41219 5.20446
88 1MJJ HAL 0.02961 0.40645 5.20446
89 1SO0 GAL 0.01199 0.40448 5.20446
90 3WV6 GAL BGC 0.001027 0.40194 5.20446
91 3ZJ0 ACO 0.02388 0.41221 5.33981
92 5I0U DCY 0.004996 0.42789 5.5
93 2AGC DAO 0.001295 0.45557 5.55556
94 4AZW ATP 0.004087 0.44417 5.57621
95 2XN5 FUN 0.005634 0.42475 5.57621
96 2XN3 ID8 0.002429 0.42303 5.57621
97 4JWH SAH 0.01994 0.41008 5.57621
98 4IXH IMP 0.03305 0.40279 5.57621
99 2E27 AB0 0.003566 0.43787 5.88235
100 1XVB BHL 0.01607 0.43539 5.88235
101 4LRJ ANP 0.01542 0.4084 5.91716
102 3LLI FAD 0.00496 0.45193 5.94796
103 3T58 FAD 0.01176 0.43379 5.94796
104 3E8T UQ8 0.04223 0.42297 5.94796
105 4PFC 2QX 0.01896 0.41758 5.94796
106 3ZDS HMQ 0.01491 0.40248 5.94796
107 5T2Z 017 0.02475 0.4153 6.06061
108 4REF 3N0 0.01826 0.40048 6.25
109 5C4L 4XR 0.02114 0.42145 6.3197
110 2OVD DAO 0.005662 0.41823 6.3197
111 5FXD H7Y 0.01995 0.40448 6.3197
112 4EIL FOL 0.02128 0.40179 6.3197
113 5A67 3PO 0.003199 0.43222 6.60377
114 5DG2 GAL GLC 0.006799 0.42611 6.66667
115 3IX8 TX3 0.02805 0.40758 6.93642
116 4NFN 2KC 0.003278 0.44382 7.0632
117 2PYW ADP 0.009918 0.42271 7.0632
118 4OIC A8S 0.01302 0.41361 7.0632
119 5IH9 6BF 0.03915 0.40972 7.0632
120 3OG9 MLT 0.009218 0.40647 7.17703
121 1TT8 PHB 0.003674 0.45528 7.31707
122 2YKL NLD 0.01141 0.41263 7.43494
123 5CYV WCA 0.006491 0.43893 7.53425
124 1J3R 6PG 0.002773 0.40325 7.80669
125 3OJI PYV 0.021 0.4085 7.93651
126 2PCU ASP 0.01545 0.40024 8.17844
127 1MDC PLM 0.0008709 0.48393 8.55019
128 5ML3 DL3 0.005969 0.45829 8.55019
129 5L9G MO0 0.02365 0.40303 8.55019
130 3ZXE PGZ 0.005031 0.40871 9.02256
131 3KDU NKS 0.007169 0.46148 9.29368
132 2P54 735 0.01392 0.42603 9.29368
133 2AG4 OLA 0.0451 0.42536 9.29368
134 1CX4 CMP 0.008983 0.42288 9.66543
135 3G08 FEE 0.04957 0.41826 10.0372
136 3WG3 A2G GAL NAG FUC 0.008684 0.41346 10.1124
137 5T8U LPA 0.01525 0.40528 10.4089
138 4QJP V1F 0.0123 0.4266 11.0266
139 3FW4 CAQ 0.009945 0.43328 11.236
140 4WN5 MVC 0.009894 0.42842 11.3043
141 3VV1 GAL FUC 0.001334 0.44682 11.875
142 1LQY BB2 0.009178 0.42336 12.5
143 5K2M ADP 0.02191 0.41081 15.0943
144 4RLT FSE 0.00676 0.4235 17.6871
145 5X8Q 82R 0.01944 0.41288 22.7273
146 2DYR TGL 0.02269 0.42211 28.2609
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