Receptor
PDB id Resolution Class Description Source Keywords
2NP9 2.45 Å EC: 1.13.11.- CRYSTAL STRUCTURE OF A DIOXYGENASE IN THE CROTONASE SUPERFAM STREPTOMYCES TOYOCAENSIS PROTEIN INHIBITOR COMPLEX OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR COFACTOR-INDEPENDENT DIOXYGENA VANCOMYCIN BIOSYNTHESIS. NATURE V. 447 342 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
OXY A:888;
B:888;
C:888;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
31.999 O2 O=O
YE1 A:999;
B:999;
C:999;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 2.7 uM
900.615 C29 H43 N8 O19 P3 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2NP9 2.45 Å EC: 1.13.11.- CRYSTAL STRUCTURE OF A DIOXYGENASE IN THE CROTONASE SUPERFAM STREPTOMYCES TOYOCAENSIS PROTEIN INHIBITOR COMPLEX OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR COFACTOR-INDEPENDENT DIOXYGENA VANCOMYCIN BIOSYNTHESIS. NATURE V. 447 342 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NP9 Ki = 2.7 uM YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
2 5KAG - YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NP9 Ki = 2.7 uM YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
2 5KAG - YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NP9 Ki = 2.7 uM YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
2 5KAG - YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YE1; Similar ligands found: 141
No: Ligand ECFP6 Tc MDL keys Tc
1 YE1 1 1
2 SCO 0.8125 0.965517
3 COA 0.809524 0.965517
4 0T1 0.809524 0.965517
5 DCA 0.808 0.943182
6 30N 0.804688 0.884211
7 CMX 0.79845 0.965517
8 ETB 0.793651 0.910112
9 COS 0.790698 0.94382
10 AMX 0.790698 0.976744
11 CAO 0.790698 0.933333
12 FAM 0.778626 0.94382
13 FCX 0.778626 0.933333
14 ACO 0.778626 0.933333
15 BCA 0.773723 0.977273
16 HAX 0.772727 0.94382
17 FYN 0.766917 0.965517
18 3KK 0.766917 0.94382
19 MCD 0.761194 0.94382
20 COK 0.761194 0.94382
21 SOP 0.761194 0.94382
22 OXK 0.761194 0.94382
23 CA6 0.761194 0.857143
24 4CA 0.76087 0.977273
25 CMC 0.755556 0.94382
26 CO6 0.755556 0.94382
27 1VU 0.755556 0.933333
28 NMX 0.755556 0.893617
29 BYC 0.753623 0.965909
30 SCD 0.75 0.965517
31 CAJ 0.75 0.94382
32 2MC 0.75 0.903226
33 FAQ 0.748201 0.965909
34 MLC 0.744526 0.94382
35 BCO 0.744526 0.94382
36 3HC 0.744526 0.954545
37 1HE 0.744526 0.923077
38 IVC 0.744526 0.954545
39 A1S 0.744526 0.94382
40 3CP 0.741007 0.94382
41 COW 0.741007 0.955056
42 COO 0.73913 0.94382
43 MCA 0.73913 0.933333
44 CAA 0.73913 0.954545
45 2CP 0.733813 0.933333
46 SCA 0.733813 0.94382
47 MC4 0.733813 0.893617
48 2NE 0.732394 0.966292
49 S0N 0.732394 0.965909
50 HGG 0.728571 0.94382
51 CA8 0.728571 0.876289
52 1GZ 0.728571 0.933333
53 2KQ 0.728571 0.923077
54 IRC 0.728571 0.954545
55 COF 0.728571 0.923077
56 4CO 0.727273 0.977273
57 HXC 0.71831 0.923077
58 GRA 0.71831 0.94382
59 WCA 0.717241 0.966292
60 0FQ 0.715278 0.965909
61 TGC 0.713287 0.933333
62 CIC 0.708333 0.94382
63 CO8 0.708333 0.923077
64 1CZ 0.708333 0.933333
65 HFQ 0.707483 0.966292
66 ST9 0.703448 0.923077
67 MYA 0.703448 0.923077
68 DCC 0.703448 0.923077
69 5F9 0.703448 0.923077
70 MFK 0.703448 0.923077
71 UCC 0.703448 0.923077
72 4KX 0.70068 0.934066
73 0ET 0.69863 0.923077
74 01A 0.69863 0.923913
75 CS8 0.693878 0.913043
76 1CV 0.693878 0.94382
77 HDC 0.689189 0.923077
78 NHM 0.689189 0.923077
79 NHW 0.689189 0.923077
80 UOQ 0.689189 0.923077
81 MRR 0.684564 0.923077
82 MRS 0.684564 0.923077
83 YNC 0.68 0.933333
84 DAK 0.68 0.934066
85 1HA 0.679739 0.966292
86 8Z2 0.675497 0.913043
87 NHQ 0.666667 0.954545
88 COD 0.656716 0.954023
89 01K 0.653846 0.94382
90 COT 0.649682 0.965909
91 93P 0.648148 0.955056
92 CA3 0.641509 0.965909
93 CCQ 0.64 0.903226
94 CA5 0.631902 0.923913
95 93M 0.628743 0.955056
96 UCA 0.618182 0.944444
97 CO7 0.610738 0.94382
98 OXT 0.590909 0.904255
99 4BN 0.575419 0.904255
100 5TW 0.575419 0.904255
101 JBT 0.559783 0.885417
102 BSJ 0.553073 0.934066
103 PAP 0.544715 0.802326
104 HMG 0.5375 0.911111
105 PLM COA 0.530864 0.891304
106 COA MYR 0.530864 0.891304
107 COA PLM 0.530864 0.891304
108 PPS 0.496124 0.726316
109 A3P 0.495935 0.790698
110 SFC 0.482353 0.944444
111 RFC 0.482353 0.944444
112 0WD 0.48 0.8
113 191 0.463415 0.838384
114 ACE SER ASP ALY THR NH2 COA 0.44898 0.901099
115 PTJ 0.439716 0.862069
116 3AM 0.435484 0.77907
117 PUA 0.427673 0.831461
118 A22 0.427536 0.825581
119 A2D 0.421875 0.813953
120 PAJ 0.421429 0.873563
121 3OD 0.41958 0.816092
122 SAP 0.41791 0.777778
123 AGS 0.41791 0.777778
124 ATR 0.41791 0.790698
125 ATP 0.413534 0.813953
126 ADP 0.412214 0.813953
127 AQP 0.410448 0.813953
128 5FA 0.410448 0.813953
129 A2R 0.410072 0.804598
130 NJP 0.407643 0.83908
131 NA7 0.405594 0.848837
132 OAD 0.405594 0.816092
133 BA3 0.40458 0.813953
134 AP5 0.401515 0.813953
135 B4P 0.401515 0.813953
136 ANP 0.40146 0.795455
137 YAP 0.401361 0.83908
138 48N 0.401316 0.8
139 AR6 0.4 0.793103
140 APR 0.4 0.793103
141 2A5 0.4 0.837209
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2np9.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found: 173
This union binding pocket(no: 2) in the query (biounit: 2np9.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.00956 0.46692 None
2 2BII MTV 0.000225 0.43369 1.17925
3 3MAG 3MA 0.00612 0.46848 1.30293
4 3MAG SAH 0.003001 0.40679 1.30293
5 3QV9 QV7 0.00377 0.44321 1.36364
6 1IA7 BGC BGC 0.03886 0.42912 1.36364
7 2CFA FAD 0.001815 0.40735 1.38249
8 4P53 NAI 0.0004074 0.41121 1.42857
9 1V6A TRE 0.0003576 0.48965 1.50602
10 1Y42 TYR 0.009836 0.41922 1.53061
11 3P7I P7I 0.01018 0.41856 1.55763
12 4M51 BEZ 0.002937 0.46859 1.59091
13 4RJK PYR 0.009843 0.44202 1.59091
14 4FWE FAD 0.0002774 0.41742 1.59091
15 3NKS FAD 0.0006253 0.40041 1.81818
16 3KJQ B94 0.0006148 0.45453 1.82927
17 2Q8H TF4 0.0003143 0.52778 1.9656
18 1E5F PLP 0.00436 0.41201 1.9802
19 3O2K DST 0.01102 0.41704 2.04545
20 3OND NAD 0.0006553 0.41059 2.04545
21 3OND ADN 0.0006553 0.41059 2.04545
22 3O2K QRP 0.01414 0.40362 2.04545
23 1T10 F6P 0.03303 0.40014 2.04545
24 3ZPG 5GP 0.00004977 0.56979 2.09424
25 1VDC FAD 0.0008556 0.40717 2.1021
26 1MZV AMP 0.003153 0.43067 2.12766
27 2Y6P CTP 0.01181 0.40687 2.13675
28 4OYA 1VE 0.0003127 0.45017 2.27273
29 3TFC PEP 0.003552 0.43872 2.33766
30 2JFV FLC 0.02197 0.41317 2.4055
31 2O2C G6Q 0.002697 0.41996 2.5
32 1ZK7 FAD 0.0007789 0.40643 2.5
33 3P3N AKG 0.00514 0.44295 2.5788
34 1G8S MET 0.03113 0.40597 2.6087
35 2EB5 OXL 0.002368 0.45876 2.62172
36 2YC5 6BC 0.00007269 0.42395 2.63158
37 3I0O ADP 0.001075 0.45002 2.65487
38 3I0O SMI 0.01431 0.41681 2.65487
39 1QZZ SAM 0.003492 0.41982 2.6738
40 1KTC NGA 0.0006623 0.4708 2.71605
41 4F8L GAL 0.02655 0.44126 2.75862
42 1FW1 GSH 0.01052 0.40105 2.77778
43 1HDR NAD 0.001172 0.40405 2.86885
44 1U5R ATP 0.004611 0.41108 2.87356
45 2ZWS PLM 0.01265 0.45991 2.95455
46 1Q11 TYE 0.003481 0.43911 2.95699
47 1UF5 CDT 0.008908 0.41196 2.9703
48 4FR3 0V4 0.001015 0.41996 2.99145
49 3SHR CMP 0.01057 0.40888 3.01003
50 1QO0 BMD 0.01724 0.41816 3.06122
51 3FC4 EDO 0.0008787 0.41131 3.18182
52 3DGB MUC 0.007355 0.41116 3.40314
53 3UEC ALA ARG TPO LYS 0.01788 0.42287 3.42466
54 1TIW TFB 0.0003843 0.4076 3.48837
55 1TIW FAD 0.0003843 0.4076 3.48837
56 3DG6 MUC 0.008681 0.40432 3.54223
57 1RZM E4P 0.001022 0.48346 3.5503
58 1RZM PEP 0.002202 0.44786 3.5503
59 1QDS PGA 0.006193 0.41852 3.58566
60 2Q09 DI6 0.01807 0.40322 3.60577
61 2IZ1 ATR 0.01426 0.42206 3.63636
62 1O0S NAI 0.000597 0.41981 3.63636
63 4CCO OGA 0.0125 0.41463 3.63636
64 4O8A FAD 0.0003066 0.40027 3.63636
65 1EJE FMN 0.005816 0.40001 3.64583
66 4B9E FAH 0.008179 0.43948 3.65448
67 4M5P MLA 0.004986 0.47338 3.6855
68 4M5P 23W 0.0288 0.41828 3.6855
69 1T26 NAI 0.001384 0.42675 3.72671
70 1T26 GBD 0.001384 0.42675 3.72671
71 4K30 NLG 0.007883 0.42347 3.75
72 1TV5 ORO 0.007011 0.40231 3.83747
73 1H82 GZZ 0.000327 0.42936 3.86364
74 1H82 FAD 0.0002707 0.42936 3.86364
75 4HA6 FAD 0.0006602 0.40649 3.86364
76 1SQ5 ADP 0.003909 0.42222 3.8961
77 1SQ5 PAU 0.02623 0.40035 3.8961
78 2WMO GTP 0.002525 0.42533 3.97196
79 1O9U ADZ 0.0003176 0.52754 4
80 2JBH 5GP 0.003245 0.43513 4
81 1XVA SAM 0.003546 0.40423 4.10959
82 2QCX PF1 0.01358 0.41786 4.18251
83 4KCT PYR 0.001006 0.45682 4.31818
84 4KCT FDP 0.01068 0.40461 4.31818
85 1C1L GAL BGC 0.01047 0.43425 4.37956
86 4OB6 S2T 0.001065 0.43532 4.39883
87 1SAY PYR 0.009987 0.4063 4.43213
88 1Z44 NPO 0.009691 0.46658 4.43787
89 1Z44 FMN 0.00283 0.4234 4.43787
90 1Z41 FMN 0.002542 0.42093 4.43787
91 1I0Z OXM 0.02439 0.4283 4.5045
92 3A1I UNU 0.004464 0.42441 4.54545
93 4JWX 1N4 0.001828 0.45141 4.64286
94 2BES RES 0.005893 0.41504 4.65116
95 3I8P 840 0.001448 0.43024 4.68384
96 4PTZ FMN 0.005949 0.40317 4.71204
97 2IYG FMN 0.0006504 0.45355 4.83871
98 4COQ SAN 0.003454 0.45106 4.8583
99 2GJN FMN 0.001127 0.40416 4.87805
100 3RO7 TDR 0.006284 0.40558 4.90566
101 2NCD ADP 0.0003546 0.48982 5
102 3JQ3 ADP 0.002883 0.43228 5.19126
103 1Y9Q MED 0.01292 0.42408 5.20833
104 1W7J ADP BEF 0.0001799 0.4595 5.29801
105 3F81 STT 0.02587 0.42695 5.46448
106 2Q37 3AL 0.004086 0.44161 5.52486
107 1I2L DCS 0.002784 0.40794 5.57621
108 1REO FAD 0.0005212 0.40503 5.68182
109 2A2X NA9 0.003559 0.40773 5.79151
110 5B5S BOG 0.01128 0.45905 5.7971
111 4E28 9MZ 0.02025 0.41485 5.84615
112 1SS4 GSH 0.003202 0.49959 5.88235
113 1SS4 CIT 0.003758 0.46702 5.88235
114 2O66 FLC 0.001174 0.46622 5.92593
115 1Y75 NAG 0.003841 0.43201 5.9322
116 1CKM GTP 0.002731 0.43833 6.06061
117 1SJW NGV 0.006306 0.4059 6.25
118 1NYT NAP 0.0006828 0.41096 6.27306
119 1J2Z SOG 0.00702 0.40229 6.2963
120 3NOJ PYR 0.008529 0.42447 6.30252
121 1ZJ6 G3D 0.003135 0.42608 6.41711
122 2C2A ADP 0.003999 0.40958 6.58915
123 4L7I SAM 0.005832 0.40349 6.59091
124 2OFE NAG 0.01434 0.42194 6.81818
125 2C5S AMP 0.009711 0.41479 6.81818
126 1R6D NAD 0.00138 0.40541 6.82493
127 3QDY A2G GAL 0.001792 0.47943 6.99301
128 3QDT A2G GAL 0.002242 0.47451 6.99301
129 3QDY CBS 0.002288 0.46643 6.99301
130 2Y7G AAE 0.002348 0.42225 7.0922
131 3LZW NAP 0.0009125 0.41411 7.22892
132 3LZW FAD 0.0003839 0.40761 7.22892
133 2YYJ 4HP 0.004053 0.40626 7.5
134 2YYJ FAD 0.004053 0.40626 7.5
135 1SB8 NAD 0.001003 0.40513 7.67045
136 1A8S PPI 0.01202 0.40452 7.69231
137 1QD0 RR6 0.002726 0.42852 7.8125
138 4IXW IXW 0.01409 0.40786 7.87402
139 2Z9V PXM 0.01412 0.41228 7.90816
140 1YOA FMN 0.01377 0.45778 8.1761
141 4WVH ASP HIS ASP ALA HIS ALA 0.00262 0.43909 8.18182
142 1EYE PMM 0.002539 0.42977 8.21429
143 3RF4 FUN 0.000072 0.51315 8.62069
144 2V5E SCR 0.01091 0.45469 8.91089
145 1KYQ NAD 0.0002858 0.44729 9.12409
146 3BY8 MLT 0.0003155 0.50828 9.15493
147 2F2U M77 0.00209 0.43807 9.54545
148 1W3R PYR 0.0009476 0.49339 9.72222
149 1ULE GLA GAL NAG 0.003689 0.46358 10
150 3LTW HLZ 0.003096 0.4533 10
151 3CF6 SP1 0.006016 0.40668 10.1796
152 1TUV VK3 0.0004763 0.5183 10.5263
153 2Y7P SAL 0.0003064 0.48552 10.5505
154 1EB9 HBA 0.003117 0.42618 11.4504
155 1MXI SAH 0.001553 0.42075 11.875
156 2E1A MSE 0.00405 0.43102 12
157 1S8F GDP 0.0006323 0.44885 12.4294
158 1T0S BML 0.0306 0.41693 12.7907
159 3F8C HT1 0.03197 0.4008 13.4921
160 1YRX FMN 0.0006709 0.44784 14.0496
161 1WDA BAG 0.004654 0.42844 14.3182
162 3I51 45C 0.005733 0.41552 14.4444
163 2C7G ODP 0.0005838 0.41752 15.7895
164 1XE7 GUN 0.0118 0.445 17.734
165 2QLX RM4 0.006796 0.44341 20.3704
166 3KPE TM3 0.007417 0.43545 20.5128
167 1N9L FMN 0.002367 0.41413 22.0183
168 4F4S EFO 0.001073 0.46159 22.3684
169 2PR5 FMN 0.002489 0.41335 24.2424
170 1XX4 BAM 0.0108 0.44703 24.5211
171 1SG4 CO8 0.000000232 0.4695 31.1538
172 1NZY BCA 0.000009915 0.43118 33.4572
173 4IZC 1GZ 0.0000000002957 0.60042 33.8182
Pocket No.: 3; Query (leader) PDB : 2NP9; Ligand: YE1; 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: 2np9.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2NP9; Ligand: YE1; 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: 2np9.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found: 19
This union binding pocket(no: 5) in the query (biounit: 2np9.bio2) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3X01 AMP 0.01439 0.43244 1.52672
2 1WOG 16D 0.04278 0.41229 1.96721
3 4XH0 ADP 0.03508 0.41005 2.23325
4 4CS9 AMP 0.01434 0.42391 2.6455
5 2JAP J01 0.028 0.41048 3.23887
6 4URN NOV 0.03936 0.40761 5.33333
7 1ON3 MCA 0.0003181 0.41255 8.63636
8 2FKA BEF 0.03027 0.4102 9.30233
9 5J6Y GLC 0.01177 0.42664 10.1064
10 5J6Y BGC 0.01177 0.42664 10.1064
11 3BPX SAL 0.0246 0.41616 10.8108
12 5JBX COA 0.000001232 0.46008 17.2414
13 4QIJ 1HA 0.00009246 0.49731 30.5389
14 4I4Z 2NE 0.0000186 0.4926 32.7273
15 1JXZ BCA 0.00001556 0.46727 33.0855
16 1DUB CAA 0.000001488 0.41059 34.8659
17 2VSS ACO 0.0000001968 0.47159 36.5942
18 2VSU ACO 0.0000001487 0.47484 36.7273
19 4I42 1HA 0.0001976 0.47185 37.5439
Pocket No.: 6; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2np9.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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