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Receptor
PDB id Resolution Class Description Source Keywords
4JWK 1.87 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDYL-TRNA HYDROLASE ACINETOBACTER BAUMANNII WITH CYTIDINE AT 1.87 A RESOLUTION ACINETOBACTER BAUMANNII ATCC 19606 = CORGANISM_TAXID: 575584 PROTEIN SYNTHESIS COMPLEX HYDROLASE
Ref.: THE MODE OF INHIBITOR BINDING TO PEPTIDYL-TRNA HYDR BINDING STUDIES AND STRUCTURE DETERMINATION OF UNBO BOUND PEPTIDYL-TRNA HYDROLASE FROM ACINETOBACTER BA PLOS ONE V. 8 67547 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CTN A:201;
Valid;
none;
Kd = 5.3 nM
243.217 C9 H13 N3 O5 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JWK 1.87 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDYL-TRNA HYDROLASE ACINETOBACTER BAUMANNII WITH CYTIDINE AT 1.87 A RESOLUTION ACINETOBACTER BAUMANNII ATCC 19606 = CORGANISM_TAXID: 575584 PROTEIN SYNTHESIS COMPLEX HYDROLASE
Ref.: THE MODE OF INHIBITOR BINDING TO PEPTIDYL-TRNA HYDR BINDING STUDIES AND STRUCTURE DETERMINATION OF UNBO BOUND PEPTIDYL-TRNA HYDROLASE FROM ACINETOBACTER BA PLOS ONE V. 8 67547 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4JWK Kd = 5.3 nM CTN C9 H13 N3 O5 C1=CN(C(=O....
2 4JX9 Kd = 1.4 nM URI C9 H12 N2 O6 C1=CN(C(=O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4JWK Kd = 5.3 nM CTN C9 H13 N3 O5 C1=CN(C(=O....
2 4JX9 Kd = 1.4 nM URI C9 H12 N2 O6 C1=CN(C(=O....
3 4QD3 Kd = 0.00000145 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
4 4QBK Kd = 0.00000145 M 3NZ C20 H25 N7 O5 COc1ccc(cc....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4JWK Kd = 5.3 nM CTN C9 H13 N3 O5 C1=CN(C(=O....
2 4JX9 Kd = 1.4 nM URI C9 H12 N2 O6 C1=CN(C(=O....
3 4QD3 Kd = 0.00000145 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
4 4QBK Kd = 0.00000145 M 3NZ C20 H25 N7 O5 COc1ccc(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CTN; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 CTN 1 1
2 AR3 1 1
3 I5A 0.754717 0.920635
4 DKZ 0.719298 0.863636
5 C 0.672131 0.842857
6 C5P 0.672131 0.842857
7 CAR 0.672131 0.842857
8 C3P 0.655738 0.828571
9 CDP 0.636364 0.857143
10 HF4 0.608696 0.857143
11 CTP 0.608696 0.857143
12 C2P 0.603175 0.842857
13 7XL 0.575342 0.859155
14 C C C C 0.564103 0.857143
15 C2G 0.552632 0.871429
16 CTD 0.551724 0.887097
17 C5G 0.55 0.859155
18 5AE 0.542373 0.935484
19 GEO 0.532258 0.878788
20 C C 0.525641 0.842857
21 DCZ 0.52459 0.907692
22 LDC 0.52459 0.907692
23 CDM 0.518519 0.813333
24 F01 0.516129 0.924242
25 CDC 0.506173 0.728395
26 URI 0.5 0.919355
27 CSV 0.494253 0.821918
28 CSQ 0.494253 0.821918
29 CXY 0.488095 0.833333
30 NVG 0.476744 0.810811
31 URD 0.47541 0.809524
32 V12 0.470588 0.833333
33 2TU 0.460317 0.848485
34 LTT 0.453125 0.876923
35 CJB 0.453125 0.873016
36 CC7 0.452055 0.802817
37 3TC 0.446154 0.835821
38 1AA 0.445652 0.8
39 16B 0.444444 0.783784
40 ZEB 0.435484 0.919355
41 G C 0.427184 0.759494
42 DC 0.424658 0.756757
43 DCM 0.424658 0.756757
44 DHZ 0.421875 0.919355
45 BRD 0.415385 0.870968
46 GPC 0.415094 0.722892
47 A C A C 0.411215 0.779221
48 PMT 0.41 0.75
49 MCN 0.403846 0.722892
50 7LS 0.402174 0.852941
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JWK; Ligand: CTN; Similar sites found with APoc: 170
This union binding pocket(no: 1) in the query (biounit: 4jwk.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 2V1O COA None
3 5SVV FMN None
4 2ZFU SAH None
5 3KFC 61X 1.5544
6 4XB2 HSE 1.5544
7 4XB2 NDP 1.5544
8 3D72 FAD 2.01342
9 5G3U ITW 2.07254
10 5ZBC FAD 2.07254
11 6BMM OLB 2.07254
12 4CFP NAG AMU NAG AMV 2.07254
13 3JZB 4HY 2.07254
14 3B8X G4M 2.07254
15 3KMZ EQO 2.59067
16 2LBD REA 2.59067
17 1V1A ADP 2.59067
18 4N9I PCG 2.59067
19 1QNF FAD 2.59067
20 1JV1 UD1 2.59067
21 1CF2 NAP 2.59067
22 1QM5 GLC GLC GLC PO4 SGC GLC 2.59067
23 5M58 SAH 2.59067
24 1N46 PFA 2.59067
25 4WUJ FMN 2.72109
26 2CYE COA 3.00752
27 2NXW TPP 3.10881
28 2A92 NAI 3.10881
29 2HW1 ANP 3.10881
30 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 3.10881
31 4NZF ARB 3.10881
32 4MGB XDH 3.10881
33 2BD0 NAP 3.10881
34 4BAE RWX 3.10881
35 4PIV 2W4 3.10881
36 2PHX MAN MAN MAN MAN 3.10881
37 2PHW MAN MAN MAN BMA MAN MAN MAN 3.10881
38 1Q8V MAN MAN MAN 3.10881
39 2PHR MAN MAN BMA MAN 3.10881
40 2PHF MAN MAN BMA MAN 3.10881
41 2PHT MAN MAN MAN BMA MAN 3.10881
42 3NC9 TR3 3.10881
43 3DRW AMP 3.10881
44 4XO8 KGM 3.16456
45 2HMT NAI 3.47222
46 6A5Y 9R0 3.62694
47 4GUS FAD 3.62694
48 2A3I C0R 3.62694
49 4GUT FAD 3.62694
50 4FWE FAD 3.62694
51 1CX4 CMP 3.62694
52 3BEJ MUF 3.62694
53 4AUT FAD 3.62694
54 3LLI FAD 3.62694
55 4EWH T77 3.62694
56 4HSU FAD 3.62694
57 1BYG STU 3.62694
58 5DRB 5FJ 3.62694
59 4UDB CV7 3.62694
60 2B3D FAD 3.62694
61 5WO4 B7V 3.62694
62 4OIV XX9 3.62694
63 3DCT 064 3.62694
64 2Y88 2ER 3.62694
65 3E8N VRA 3.62694
66 3E8N ATP 3.62694
67 1ZK4 NAP 3.62694
68 4HA9 NDP 3.62694
69 1JQI CAA 3.62694
70 1XKQ NDP 3.62694
71 1VEM GLC GLC 3.62694
72 1N9L FMN 3.66972
73 2Z6C FMN 3.87597
74 4YV5 SVR 4.09836
75 3QCP FAD 4.14508
76 3L0E G58 4.14508
77 5HMY LNY 4.14508
78 4GFD 0YB 4.14508
79 5MWY YNU 4.14508
80 5ZZ6 NAD 4.14508
81 2GZM DGL 4.14508
82 3ABI NAD 4.14508
83 1DKF BMS 4.14508
84 1YC5 NCA 4.14508
85 3FRH SAH 4.34783
86 3FAL LO2 4.66321
87 3HKW IX6 4.66321
88 2WCU FUC 4.69799
89 3HGM ATP 4.7619
90 5X9D 80F 5.18135
91 2VAT COA 5.18135
92 4J4H NAI 5.18135
93 2I7C AAT 5.18135
94 1YY5 FAD 5.69948
95 1U1I NAD 5.69948
96 3SRV S19 5.69948
97 2PT9 2MH 5.69948
98 2Z6D FMN 6.15385
99 3ZNN FAD 6.21762
100 3ZNN 4WL 6.21762
101 2BVL GLC 6.21762
102 2BVL UDP 6.21762
103 3WBF NAP 6.21762
104 3WBF API 6.21762
105 5DH3 5BS 6.21762
106 4P8K 38C 6.73575
107 4P8K FAD 6.73575
108 1LUA NAP 6.73575
109 2ZWI C5P 6.73575
110 3SHR CMP 6.73575
111 3GWN FAD 7.01754
112 1QSR ACO 7.25389
113 3CW9 01A 7.25389
114 1JI0 ATP 7.25389
115 2IVD FAD 7.77202
116 1M2Z DEX 7.77202
117 5G5W R8C 7.77202
118 2FYU FDN 7.77202
119 2REG CHT 7.77202
120 3BQD DAY 7.77202
121 2H7C COA 8.29016
122 5H1W LER 8.29016
123 2F2H XTG 8.29016
124 6GBV FMN 8.29016
125 5FXD H7Y 8.29016
126 3N1S 5GP 8.40336
127 4R38 RBF 8.57143
128 6F3M NAD 8.80829
129 3LXN MI1 8.80829
130 2PR5 FMN 9.09091
131 3I59 N6R 9.32642
132 6FX0 E9T 9.32642
133 2Q6B HR2 9.32642
134 1RE8 BD2 9.32642
135 3I54 CMP 9.32642
136 3P7N FMN 9.32642
137 5BO9 CSF 9.32642
138 2A19 ANP 10.3627
139 5T67 SAH 10.3627
140 3UP3 XCA 10.3627
141 5L95 AMP 10.3627
142 3RUV ANP 10.3627
143 4PVV HO4 10.8808
144 4WW7 AMP 10.8808
145 1KQF MGD 11.399
146 3C3N FMN 12.4352
147 6A56 LAT 12.8049
148 1SR7 MOF 12.9534
149 3RGA LSB 12.9534
150 3T50 FMN 13.2812
151 5YU3 PRO 13.4715
152 5YU3 NAD 13.4715
153 6GG9 FMN 13.4715
154 2Y3S TIR 13.4715
155 4P6X HCY 14.5078
156 3GN8 DEX 15.0259
157 5UFS 1TA 15.0259
158 1RSG FAD 15.0259
159 4E2J MOF 15.0259
160 3CXH SMA 15.0794
161 3CX5 SMA 15.0794
162 3EKK GS2 15.544
163 3O3O 2RH 17.0984
164 4PLT NAI 17.6166
165 4PLT OXM 17.6166
166 4A01 2PN 18.1347
167 5LXT ACP 19.6891
168 6C7Y ADP 20.5128
169 2PX6 DH9 22.2798
170 5LU5 M7P 27.9793
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