Receptor
PDB id Resolution Class Description Source Keywords
1NC1 2 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF E. COLI MTA/ADOHCY NUCLEOSIDASE COMPLEXED WITH 5'-METHYLTHIOTUBERCIDIN (MTH) ESCHERICHIA COLI MIXED ALPHA/BETA DIMER HYDROLASE
Ref.: STRUCTURE OF ESCHERICHIA COLI 5'-METHYLTHIOADENOSINE/ S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE INHIBITOR COMPLEXES PROVIDE INSIGHT INTO THE CONFORMATIONAL CHANGES REQUIRED FOR SUBSTRATE BINDING AND CATALYSIS. J.BIOL.CHEM. V. 278 8761 200
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTH A:233;
B:234;
Valid;
Valid;
none;
none;
Ki = 0.75 uM
296.345 C12 H16 N4 O3 S CSC[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4WKC 1.64 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF ESCHERICHIA COLI 5'-METHYLTHIOADENOSINE ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH BUD ADME-IMMUCILLIN-A ESCHERICHIA COLI O139:H28 HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: ACTIVE SITE AND REMOTE CONTRIBUTIONS TO CATALYSIS I METHYLTHIOADENOSINE NUCLEOSIDASES. BIOCHEMISTRY V. 54 2520 2015
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3DF9 - DF9 C19 H23 N5 O S c1ccc(cc1)....
2 4F1W - ADE C5 H5 N5 c1[nH]c2c(....
3 1Y6Q Ki = 2 pM TDI C13 H19 N5 O S CSC[C@H]1C....
4 4YML Ki = 4.5 nM 4F0 C13 H19 N5 O S CSC[C@@H]1....
5 1NC3 Ki = 10 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
6 4WKC Ki = 0.21 pM BIG C16 H25 N5 O S CCCCSC[C@H....
7 1JYS Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
8 4F2W Ki = 5 pM TDI C13 H19 N5 O S CSC[C@H]1C....
9 1NC1 Ki = 0.75 uM MTH C12 H16 N4 O3 S CSC[C@@H]1....
10 1Z5N Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
11 4F2P Ki = 5 pM 2EL C16 H25 N5 O3 S c1c(c2c([n....
12 1Y6R Ki = 77 pM MTM C12 H19 N5 O2 S CSC[C@@H]1....
13 4F3C Ki = 1.5 pM BIG C16 H25 N5 O S CCCCSC[C@H....
14 4F3K Ki = 69 pM HCE C16 H24 N6 O3 S c1c(c2c([n....
15 1Z5O - MTA C11 H15 N5 O3 S CSC[C@@H]1....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3DF9 - DF9 C19 H23 N5 O S c1ccc(cc1)....
2 4F1W - ADE C5 H5 N5 c1[nH]c2c(....
3 1Y6Q Ki = 2 pM TDI C13 H19 N5 O S CSC[C@H]1C....
4 4YML Ki = 4.5 nM 4F0 C13 H19 N5 O S CSC[C@@H]1....
5 1NC3 Ki = 10 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
6 4WKC Ki = 0.21 pM BIG C16 H25 N5 O S CCCCSC[C@H....
7 1JYS Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
8 4F2W Ki = 5 pM TDI C13 H19 N5 O S CSC[C@H]1C....
9 1NC1 Ki = 0.75 uM MTH C12 H16 N4 O3 S CSC[C@@H]1....
10 1Z5N Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
11 4F2P Ki = 5 pM 2EL C16 H25 N5 O3 S c1c(c2c([n....
12 1Y6R Ki = 77 pM MTM C12 H19 N5 O2 S CSC[C@@H]1....
13 4F3C Ki = 1.5 pM BIG C16 H25 N5 O S CCCCSC[C@H....
14 4F3K Ki = 69 pM HCE C16 H24 N6 O3 S c1c(c2c([n....
15 1Z5O - MTA C11 H15 N5 O3 S CSC[C@@H]1....
16 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
17 3DP9 Kd = 208 pM BIG C16 H25 N5 O S CCCCSC[C@H....
18 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DF9 - DF9 C19 H23 N5 O S c1ccc(cc1)....
2 4F1W - ADE C5 H5 N5 c1[nH]c2c(....
3 1Y6Q Ki = 2 pM TDI C13 H19 N5 O S CSC[C@H]1C....
4 4YML Ki = 4.5 nM 4F0 C13 H19 N5 O S CSC[C@@H]1....
5 1NC3 Ki = 10 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
6 4WKC Ki = 0.21 pM BIG C16 H25 N5 O S CCCCSC[C@H....
7 1JYS Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
8 4F2W Ki = 5 pM TDI C13 H19 N5 O S CSC[C@H]1C....
9 1NC1 Ki = 0.75 uM MTH C12 H16 N4 O3 S CSC[C@@H]1....
10 1Z5N Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
11 4F2P Ki = 5 pM 2EL C16 H25 N5 O3 S c1c(c2c([n....
12 1Y6R Ki = 77 pM MTM C12 H19 N5 O2 S CSC[C@@H]1....
13 4F3C Ki = 1.5 pM BIG C16 H25 N5 O S CCCCSC[C@H....
14 4F3K Ki = 69 pM HCE C16 H24 N6 O3 S c1c(c2c([n....
15 1Z5O - MTA C11 H15 N5 O3 S CSC[C@@H]1....
16 1ZOS Ki = 1 uM MTM C12 H19 N5 O2 S CSC[C@@H]1....
17 4WKP - 3QA C17 H27 N5 O3 S c1c(c2c([n....
18 6DYV Kd = 0.026 nM OS3 C17 H23 N5 O S C#CCCCSC[C....
19 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
20 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
21 6DYY Kd = 0.028 nM OS6 C21 H32 N8 O S CCCCn1cc(n....
22 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
23 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
24 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
25 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
26 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
27 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
28 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
29 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
30 6DYW Kd = 0.036 nM OS5 C24 H30 N8 O S c1ccc(cc1)....
31 6DYU Kd = 0.055 nM OS2 C15 H19 N5 O S C#CCSC[C@H....
32 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
33 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
34 3DP9 Kd = 208 pM BIG C16 H25 N5 O S CCCCSC[C@H....
35 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
36 4BMZ - MTA C11 H15 N5 O3 S CSC[C@@H]1....
37 4BMX - ADE C5 H5 N5 c1[nH]c2c(....
38 3BL6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
39 6AYR Ki = 4.1 nM BIG C16 H25 N5 O S CCCCSC[C@H....
40 6AYQ Ki = 6.5 nM TDI C13 H19 N5 O S CSC[C@H]1C....
41 6AYO Ki = 5.1 nM C1Y C14 H21 N5 O CCC[C@H]1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MTH; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 MTH 1 1
2 TBN 0.775862 0.876923
3 7DD 0.564103 0.77027
4 7DT 0.54321 0.77027
5 MTA 0.520548 0.984127
6 7CH 0.463415 0.774648
7 3DH 0.4125 0.923077
Similar Ligands (3D)
Ligand no: 1; Ligand: MTH; Similar ligands found: 160
No: Ligand Similarity coefficient
1 MTM 0.9990
2 ADN 0.9782
3 A4D 0.9781
4 MTI 0.9773
5 FMC 0.9721
6 M2T 0.9703
7 IMH 0.9684
8 NOS 0.9641
9 1DA 0.9609
10 9DI 0.9584
11 TAL 0.9579
12 NWW 0.9575
13 FMB 0.9559
14 NWQ 0.9536
15 DBM 0.9534
16 N8M 0.9533
17 5NB 0.9525
18 PRH 0.9508
19 ZAS 0.9506
20 AD3 0.9496
21 5AD 0.9488
22 GMP 0.9475
23 SNI 0.9470
24 MTP 0.9465
25 MDR 0.9464
26 HPR 0.9456
27 XYA 0.9446
28 5N5 0.9446
29 6MD 0.9411
30 A 0.9406
31 8OX 0.9398
32 3AD 0.9388
33 5FD 0.9380
34 GNG 0.9373
35 FM1 0.9369
36 CFE 0.9367
37 5ID 0.9362
38 AMP 0.9360
39 NEC 0.9354
40 MCF 0.9352
41 IMG 0.9341
42 EP4 0.9332
43 5CD 0.9330
44 IMP 0.9324
45 TDI 0.9295
46 FMP 0.9287
47 3BH 0.9270
48 PUR 0.9268
49 5UD 0.9264
50 4UO 0.9256
51 2FA 0.9250
52 3D1 0.9249
53 RAB 0.9246
54 FTU 0.9226
55 C1Y 0.9217
56 5I5 0.9212
57 THM 0.9209
58 EKH 0.9204
59 13A 0.9203
60 UA2 0.9192
61 CTN 0.9190
62 Z8B 0.9187
63 6CR 0.9180
64 26A 0.9175
65 Y3J 0.9174
66 RPP 0.9161
67 URI 0.9153
68 5F1 0.9153
69 2FD 0.9143
70 FM2 0.9139
71 CL9 0.9120
72 D5M 0.9100
73 NOC 0.9072
74 8BR 0.9067
75 UUA 0.9061
76 AFX 0.9053
77 5BT 0.9052
78 MZR 0.9037
79 MG7 0.9034
80 CC5 0.9031
81 DCF 0.9021
82 DUR 0.9016
83 DCZ 0.9011
84 8HG 0.9009
85 TMP 0.9008
86 DIH 0.9001
87 DA 0.8986
88 ARJ 0.8981
89 U 0.8980
90 0DN 0.8960
91 7D7 0.8958
92 2TU 0.8952
93 5MD 0.8945
94 38B 0.8938
95 DNB 0.8935
96 4F0 0.8930
97 MCY 0.8925
98 XTS 0.8906
99 IM5 0.8902
100 5P7 0.8893
101 RBV 0.8876
102 3L1 0.8875
103 93A 0.8850
104 B86 0.8842
105 KF5 0.8832
106 ID2 0.8823
107 GA2 0.8820
108 6U5 0.8817
109 ZYV 0.8815
110 5FU 0.8803
111 ZJB 0.8798
112 CDY 0.8795
113 ACE TRP 0.8784
114 UMP 0.8783
115 PSU 0.8762
116 9UL 0.8758
117 ACK 0.8758
118 TIZ 0.8745
119 3DT 0.8743
120 OS2 0.8742
121 UFP 0.8729
122 A4G 0.8725
123 TKW 0.8723
124 I0D 0.8723
125 QQX 0.8721
126 DU 0.8714
127 NEO 0.8703
128 PIR 0.8703
129 QQY 0.8702
130 DCM 0.8689
131 NYM 0.8677
132 5IU 0.8675
133 NEU 0.8675
134 HBI 0.8673
135 8OG 0.8663
136 HDU 0.8659
137 MTE 0.8653
138 X2M 0.8646
139 KMG 0.8643
140 UMC 0.8641
141 TR7 0.8634
142 UX0 0.8634
143 4EZ 0.8626
144 DC 0.8626
145 SY4 0.8623
146 N1Y 0.8608
147 IM4 0.8608
148 DI 0.8605
149 DOC 0.8605
150 DUS 0.8604
151 TRP 0.8602
152 6OG 0.8601
153 PE2 0.8595
154 SGP 0.8595
155 THU 0.8591
156 AX8 0.8587
157 145 0.8580
158 5JT 0.8578
159 8DA 0.8575
160 BGC GLC 0.8557
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WKC; Ligand: BIG; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 4wkc.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 3LGS ADE 32.2449
2 3LGS SAH 32.2449
3 3LGS ADE 32.2449
4 3LGS SAH 32.2449
Pocket No.: 2; Query (leader) PDB : 4WKC; Ligand: BIG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4wkc.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
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