Receptor
PDB id Resolution Class Description Source Keywords
2CUN 2.1 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM PYROCOCCUS HORIKOSHII OT3 PYROCOCCUS HORIKOSHII PHOSPHOGLYCERATE KINASE STRUCTURAL GENOMICS TANPAKU 3000 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI NPPSFA NAPROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES TRAN
Ref.: CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM P HORIKOSHII OT3 TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PG A:503;
B:504;
Valid;
Valid;
none;
none;
submit data
186.057 C3 H7 O7 P C([C@...
CL A:505;
B:506;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
GOL A:501;
B:502;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MPD A:508;
A:509;
B:507;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CUN 2.1 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM PYROCOCCUS HORIKOSHII OT3 PYROCOCCUS HORIKOSHII PHOSPHOGLYCERATE KINASE STRUCTURAL GENOMICS TANPAKU 3000 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI NPPSFA NAPROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES TRAN
Ref.: CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM P HORIKOSHII OT3 TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
3 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
4 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
5 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
6 2WZC - ALF ADP 3PG n/a n/a
7 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
8 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
11 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
13 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
16 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
17 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 2WZD - AF3 ADP 3PG n/a n/a
19 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
20 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
21 2YBE - LA8 ALF 3PG n/a n/a
22 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
23 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
24 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
25 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
26 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
27 3ZLB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PG; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 3PG 1 1
2 DEZ 0.575758 0.941176
3 DER 0.575758 0.941176
4 SEP 0.515152 0.74359
5 4TP 0.5 0.780488
6 PA5 0.486486 0.941176
7 R10 0.486486 0.941176
8 DG2 0.485714 0.909091
9 LG6 0.461538 0.941176
10 6PG 0.461538 0.941176
11 HG3 0.451613 0.9375
12 1GP 0.4375 0.852941
13 G3P 0.4375 0.852941
14 PGA 0.433333 0.90625
15 DXP 0.432432 0.911765
16 M2P 0.424242 0.857143
17 G3H 0.411765 0.9375
18 5RP 0.410256 0.837838
19 D5X 0.410256 0.941176
20 5SP 0.410256 0.837838
21 HMS 0.410256 0.837838
22 0V5 0.40625 0.727273
23 PEQ 0.40625 0.727273
24 RES 0.4 0.659574
25 XBP 0.4 0.885714
26 RUB 0.4 0.885714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CUN; Ligand: 3PG; 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: 2cun.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2CUN; Ligand: 3PG; Similar sites found: 143
This union binding pocket(no: 2) in the query (biounit: 2cun.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EB4 FAD 0.02221 0.43033 1.46341
2 2Q1S NAI 0.04575 0.40083 1.59151
3 4XDA RIB 0.02816 0.40761 1.94175
4 4XDA ADP 0.02816 0.40761 1.94175
5 3GDN FAD 0.02432 0.42795 1.95122
6 3GDN HBX 0.03043 0.42795 1.95122
7 5THY SAH 0.02032 0.41029 1.97531
8 5THZ SAH 0.02538 0.4054 1.97531
9 1TB3 FMN 0.0272 0.40972 1.98864
10 2Q4H AMP 0.01721 0.41568 1.9943
11 1I8T FAD 0.01881 0.4076 2.17984
12 3UCL FAD 0.01006 0.46086 2.19512
13 3UCL CYH 0.01006 0.46086 2.19512
14 3UCL NAP 0.01074 0.46086 2.19512
15 4GA6 AMP 0.008641 0.42531 2.19512
16 5THQ NDP 0.04163 0.40276 2.20588
17 2O3Z AI7 0.04345 0.41506 2.21402
18 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 0.0041 0.44063 2.29885
19 4ZNO SUC 0.0002018 0.45673 2.38806
20 4UUG PXG 0.04169 0.40265 2.40964
21 1LYX PGA 0.006038 0.43188 2.41935
22 3ZQ6 ADP ALF 0.04341 0.40199 2.46914
23 2ZYJ PGU 0.0376 0.40982 2.51889
24 2GVC FAD 0.01018 0.44766 2.68293
25 1F74 NAY 0.007434 0.42622 2.73038
26 4Q4K FMN 0.03824 0.4037 2.80112
27 1QZR ANP 0.01946 0.40628 2.87081
28 1PS9 FAD 0.004943 0.47215 2.92683
29 5G3U ITW 0.00845 0.4602 2.92683
30 5G3U FDA 0.008283 0.45312 2.92683
31 1FEC FAD 0.0421 0.40768 2.92683
32 1PS9 FMN 0.01958 0.40445 2.92683
33 3RKR NAP 0.04881 0.40873 3.05344
34 1D6S MET PLP 0.0246 0.40148 3.10559
35 5A5D 5LC 0.01883 0.40351 3.11419
36 4MIG G3F 0.02144 0.43994 3.17073
37 1XKV ATP 0.008737 0.4324 3.17073
38 1IYE PGU 0.03452 0.4191 3.23625
39 4YDD MGD 0.0372 0.42592 3.3033
40 4YDD MD1 0.0372 0.42592 3.3033
41 1MK1 APR 0.03083 0.40384 3.38164
42 5A1S FLC 0.006087 0.41061 3.41463
43 4BI7 PGA 0.02357 0.42094 3.50195
44 2OZL TPP 0.03147 0.40492 3.51906
45 2XVE FAD 0.0227 0.44444 3.65854
46 4U7W NDP 0.02409 0.406 3.65854
47 2VVM FAD 0.002538 0.48814 3.90244
48 2R09 4IP 0.02383 0.40553 3.90244
49 5EOU ATP 0.01574 0.4056 4.03226
50 1MOQ GLP 0.02891 0.40771 4.07609
51 1C3M MAN MAN 0.0008326 0.44277 4.08163
52 5KZD RCJ 0.00476 0.43758 4.09556
53 1REO FAD 0.006547 0.46176 4.14634
54 5U8U FAD 0.0182 0.43611 4.14634
55 1V59 FAD 0.01954 0.42291 4.14634
56 3EYA FAD 0.03425 0.40154 4.14634
57 3VY6 BGC BGC 0.0004967 0.45326 4.25532
58 1Q8O MAN MMA 0.001023 0.45511 4.36508
59 1Q8P MAN MMA 0.001405 0.45252 4.36508
60 1Q8V MAN MAN 0.001588 0.44051 4.36508
61 2GN3 MAN 0.000846 0.44034 4.36508
62 2GN3 MMA 0.0009489 0.4369 4.36508
63 1Q8V MAN MAN MAN 0.002896 0.4368 4.36508
64 2GNB MAN 0.001314 0.43646 4.36508
65 2PHX MAN MAN MAN MAN 0.003607 0.43066 4.36508
66 2GMM MAN MAN 0.001227 0.43016 4.36508
67 2PHX MAN MAN 0.003295 0.42797 4.36508
68 2GNM MAN 0.001379 0.42651 4.36508
69 2PHU MAN MAN 0.00102 0.42435 4.36508
70 2GND MAN 0.001087 0.42305 4.36508
71 1UKG MMA 0.002266 0.42014 4.36508
72 1Q8Q MAN MMA 0.001724 0.41676 4.36508
73 2PHT MAN MAN MAN 0.001296 0.41101 4.36508
74 1Q8S MAN MMA 0.002372 0.4103 4.36508
75 1RSG FAD 0.0114 0.44578 4.39024
76 4BV6 FAD 0.03386 0.41808 4.63415
77 1WYV PLP AOA 0.01572 0.40289 4.63415
78 5MBX SP5 0.02051 0.43631 4.87805
79 5MBX FAD 0.02051 0.43631 4.87805
80 1N4W FAD 0.02006 0.41766 4.87805
81 2RDT FMN 0.01786 0.40929 4.90956
82 2RDT 2RD 0.02282 0.40929 4.90956
83 3AD8 NAD 0.01406 0.44131 4.9505
84 3B9Q MLI 0.003413 0.42492 4.96689
85 1XXR MAN 0.0008901 0.45048 4.96894
86 1ZGS XMM 0.0005347 0.44809 5.12195
87 2GAG NAD 0.01557 0.43501 5.2381
88 2GAG FAD 0.03369 0.41205 5.2381
89 2GAG FOA 0.03369 0.41205 5.2381
90 2OG2 MLI 0.001307 0.44651 5.29248
91 5TQZ GLC 0.002268 0.4258 5.33333
92 2VCH UDP 0.0263 0.40484 5.36585
93 3MJE NDP 0.03804 0.4048 5.36585
94 2WSB NAD 0.0357 0.40268 5.51181
95 4RPL 3UC 0.01895 0.45245 5.51378
96 4RPL FAD 0.03374 0.43459 5.51378
97 4MRT COA 0.007858 0.43867 5.55556
98 2BQP GLC 0.002326 0.42764 5.55556
99 5A0R ACE GLU VAL ASN PRO 0.03465 0.41663 5.55556
100 4YNU LGC 0.008933 0.45463 5.85366
101 4YNU FAD 0.007883 0.45463 5.85366
102 5J7X FAD 0.008784 0.44878 5.85366
103 5G5G MCN 0.03838 0.40575 6.11354
104 2AE2 NAP 0.04543 0.41216 6.15385
105 2AE2 PTO 0.04543 0.41216 6.15385
106 3LL2 MAN MAN MAN MAN MAN MAN MAN MAN 0.00192 0.45075 6.50407
107 2GUD MAN 0.0001096 0.48859 6.55738
108 2GUC MAN 0.0001172 0.4874 6.55738
109 2NU5 NAG 0.0001557 0.47864 6.55738
110 2NUO BGC 0.0002407 0.47582 6.55738
111 2HYR BGC GLC 0.0001896 0.46793 6.55738
112 2GUD BMA 0.000075 0.46209 6.55738
113 2HYQ MAN MAN 0.0005964 0.43757 6.55738
114 2AQJ TRP 0.01357 0.45642 6.82927
115 2AQJ FAD 0.0139 0.45642 6.82927
116 1YY5 FAD 0.02033 0.4301 6.82927
117 1V3S ATP 0.01171 0.42299 6.89655
118 3F8D FAD 0.005948 0.48576 7.12074
119 1LES GLC FRU 0.003574 0.41854 7.18232
120 2ZJ3 G6P 0.0388 0.4017 7.2
121 3Q9T FAY 0.001931 0.48718 7.31707
122 5AV7 MMA MAN NAG MAN NAG NAG 0.01115 0.42245 7.94702
123 1CR1 TTP 0.01382 0.40517 8.10811
124 1OFS SUC 0.002156 0.41108 8.33333
125 1KO8 6PG 0.01943 0.40537 8.57143
126 4YRY FAD 0.03647 0.41656 8.78049
127 4KAX 4IP 0.0251 0.4042 9.93789
128 1OJ7 NZQ 0.04051 0.40575 10.049
129 4MO2 FDA 0.02181 0.42538 10.0543
130 5L3S GNP 0.003663 0.44883 10.473
131 3KC1 2T6 0.007298 0.42029 10.6825
132 1OJ4 ANP 0.001323 0.46977 11.3074
133 5T2U NAP 0.02351 0.4201 13.3065
134 2F3R G5P 0.04193 0.40127 13.5266
135 2F5Z FAD 0.03055 0.40965 14.0625
136 4XVU ATP 0.01004 0.41987 14.3478
137 4XTR ATP 0.01314 0.41121 14.3478
138 1LOB MMA 0.001754 0.40583 14.3646
139 1FAO 4IP 0.02355 0.40574 16.6667
140 3WV8 ATP 0.02546 0.40674 22.0183
141 3R96 AMP 0.02342 0.41151 28.7234
142 3R96 ACO 0.02342 0.41151 28.7234
143 4GYW UDP 0.01725 0.42493 42.8571
Feedback