FAIRMol

MK153

Pose ID 8318 Compound 2730 Pose 188

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand MK153
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
25.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.43
Burial
78%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.927 kcal/mol/HA) ✓ Good fit quality (FQ -8.94) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (25.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-27.799
kcal/mol
LE
-0.927
kcal/mol/HA
Fit Quality
-8.94
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
4.74
cLogP
Final rank
2.3352
rank score
Inter norm
-1.058
normalised
Contacts
18
H-bonds 9
Strain ΔE
25.2 kcal/mol
SASA buried
78%
Lipo contact
81% BSA apolar/total
SASA unbound
620 Ų
Apolar buried
390 Ų

Interaction summary

HBD 1 HBA 6 PC 1 HY 3 PI 4 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap15Native recall0.79
Jaccard0.68RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
256 0.31638489365544653 -1.29672 -32.318 6 16 0 0.00 0.00 - no Open
253 1.8534100571059364 -1.09083 -28.6922 14 11 0 0.00 0.00 - no Open
188 2.335241481496056 -1.05817 -27.7995 9 18 15 0.79 0.43 - no Current
226 2.797223121583977 -1.02004 -25.9723 4 17 0 0.00 0.00 - no Open
383 2.9656784107887395 -0.817119 -20.7174 8 10 0 0.00 0.00 - no Open
357 3.111077451899158 -0.759397 -21.5499 5 14 0 0.00 0.00 - no Open
250 3.9521264673394088 -0.950188 -22.7349 7 19 0 0.00 0.00 - no Open
272 4.149605552322236 -1.01476 -26.5406 10 16 0 0.00 0.00 - no Open
202 4.363632399401475 -1.00063 -24.108 9 18 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -27.799kcal/mol
Ligand efficiency (LE) -0.9266kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.939
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.74
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 51.80kcal/mol
Minimised FF energy 26.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 619.7Ų
Total solvent-accessible surface area of free ligand
BSA total 483.6Ų
Buried surface area upon binding
BSA apolar 389.7Ų
Hydrophobic contacts buried
BSA polar 93.8Ų
Polar contacts buried
Fraction buried 78.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2584.0Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1387.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)