Receptor
PDB id Resolution Class Description Source Keywords
1Y6R 2.2 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF MTA/ADOHCY NUCLEOSIDASE COMPLEXED WITH MT-IMMA. ESCHERICHIA COLI MIXED ALPHA/BETA HYDROLASE
Ref.: STRUCTURAL RATIONALE FOR THE AFFINITY OF PICO- AND FEMTOMOLAR TRANSITION STATE ANALOGUES OF ESCHERICHIA COLI 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE. J.BIOL.CHEM. V. 280 18274 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTM A:233;
B:234;
 Valid;
Valid;
 none;
none;
 Ki = 77 pM
297.377 C12 H19 N5 O2 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: MTM; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 MTM 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: MTM; Similar ligands found: 147
No: Ligand Similarity coefficient
1 MTA 1.0000
2 MTH 0.9990
3 MTI 0.9793
4 M2T 0.9747
5 IMH 0.9738
6 FMC 0.9730
7 TBN 0.9721
8 ADN 0.9717
9 NOS 0.9691
10 A4D 0.9672
11 9DI 0.9670
12 FMB 0.9631
13 TAL 0.9629
14 GMP 0.9612
15 1DA 0.9597
16 AD3 0.9555
17 Z8B 0.9543
18 XYA 0.9520
19 5FD 0.9518
20 PRH 0.9494
21 DBM 0.9469
22 MDR 0.9464
23 IMG 0.9463
24 ZAS 0.9455
25 5CD 0.9454
26 FM1 0.9441
27 HPR 0.9436
28 5AD 0.9427
29 NWW 0.9420
30 AFX 0.9406
31 5NB 0.9405
32 5N5 0.9403
33 5F1 0.9385
34 Y3J 0.9382
35 IMP 0.9375
36 3AD 0.9374
37 SNI 0.9355
38 NWQ 0.9354
39 AMP 0.9347
40 TDI 0.9345
41 N8M 0.9338
42 5ID 0.9338
43 2FA 0.9330
44 A 0.9323
45 NEC 0.9320
46 MTP 0.9317
47 GNG 0.9308
48 6MD 0.9308
49 FM2 0.9294
50 FMP 0.9289
51 8OX 0.9287
52 RAB 0.9284
53 C1Y 0.9272
54 PUR 0.9258
55 3D1 0.9254
56 THM 0.9252
57 CFE 0.9245
58 6CR 0.9239
59 2FD 0.9226
60 URI 0.9205
61 NOC 0.9188
62 ARJ 0.9181
63 3DH 0.9176
64 RPP 0.9171
65 3BH 0.9141
66 FTU 0.9133
67 5UD 0.9127
68 26A 0.9126
69 D5M 0.9123
70 DCF 0.9121
71 13A 0.9120
72 EKH 0.9113
73 TMP 0.9089
74 EP4 0.9088
75 5BT 0.9084
76 CL9 0.9078
77 DNB 0.9042
78 0DN 0.9018
79 UA2 0.9010
80 5MD 0.8999
81 CC5 0.8971
82 2TU 0.8967
83 MCY 0.8962
84 MG7 0.8957
85 TIA 0.8953
86 DUR 0.8950
87 8BR 0.8942
88 4F0 0.8936
89 U 0.8930
90 DIH 0.8919
91 B86 0.8918
92 3L1 0.8890
93 IM5 0.8882
94 NYM 0.8872
95 NEO 0.8862
96 38B 0.8857
97 7D7 0.8827
98 XTS 0.8822
99 OS2 0.8804
100 TKW 0.8803
101 PIR 0.8795
102 5P7 0.8793
103 TR7 0.8792
104 8OG 0.8789
105 GA2 0.8788
106 3DT 0.8779
107 RBV 0.8778
108 ZJB 0.8777
109 ACE TRP 0.8774
110 FDM 0.8770
111 TIZ 0.8763
112 UFP 0.8755
113 A4G 0.8754
114 CDY 0.8753
115 UMP 0.8731
116 DCM 0.8727
117 X2M 0.8712
118 9UL 0.8709
119 NNR 0.8705
120 IWH 0.8704
121 4EZ 0.8701
122 QBT 0.8698
123 QQY 0.8697
124 NMN 0.8697
125 MTE 0.8686
126 DDN 0.8678
127 6TX 0.8663
128 DC 0.8658
129 SGP 0.8657
130 DA 0.8657
131 DI 0.8655
132 THU 0.8655
133 NEU 0.8654
134 0QV 0.8650
135 TRP 0.8646
136 DU 0.8634
137 ACK 0.8616
138 5IU 0.8606
139 QQX 0.8605
140 DOC 0.8600
141 BIG 0.8597
142 ZYV 0.8595
143 IM4 0.8589
144 159 0.8583
145 8DA 0.8574
146 9FN 0.8540
147 TH4 0.8516
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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