FAIRMol

MK29

Pose ID 8310 Compound 1262 Pose 180

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 MK29
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
10.7 kcal/mol
Protein clashes
7
Internal clashes
11
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.43
Burial
86%
Hydrophobic fit
88%
Reason: 11 internal clashes
7 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.025 kcal/mol/HA) ✓ Good fit quality (FQ -9.32) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Moderate strain (10.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (11)
Score
-25.635
kcal/mol
LE
-1.025
kcal/mol/HA
Fit Quality
-9.32
FQ (Leeson)
HAC
25
heavy atoms
MW
342
Da
LogP
4.31
cLogP
Final rank
1.2753
rank score
Inter norm
-1.122
normalised
Contacts
19
H-bonds 7
Strain ΔE
10.7 kcal/mol
SASA buried
86%
Lipo contact
88% BSA apolar/total
SASA unbound
602 Ų
Apolar buried
452 Ų

Interaction summary

HBD 2 HBA 5 HY 4 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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
Jaccard0.65RMSD-
HB strict3Strict recall0.33
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
180 1.2753405841528704 -1.12179 -25.6351 7 19 15 0.79 0.43 - no Current
300 2.22332971551258 -1.14752 -26.0885 5 18 0 0.00 0.00 - no Open
203 2.7620845826778937 -1.19377 -25.0678 8 19 0 0.00 0.00 - no Open
380 2.8934951626599332 -1.02286 -21.1841 6 15 0 0.00 0.00 - no Open
301 3.273343699463647 -0.792808 -17.732 6 10 0 0.00 0.00 - no Open
189 3.361396722874519 -1.0661 -25.1956 7 15 0 0.00 0.00 - no Open
247 3.6688427296143553 -1.35024 -30.2174 6 18 0 0.00 0.00 - no Open
249 4.150411199346974 -1.466 -32.3181 6 18 0 0.00 0.00 - no Open
283 4.185532692114118 -0.915922 -20.4383 7 9 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 -25.635kcal/mol
Ligand efficiency (LE) -1.0254kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.322
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 342.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.31
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 48.06kcal/mol
Minimised FF energy 37.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 601.7Ų
Total solvent-accessible surface area of free ligand
BSA total 515.4Ų
Buried surface area upon binding
BSA apolar 452.0Ų
Hydrophobic contacts buried
BSA polar 63.4Ų
Polar contacts buried
Fraction buried 85.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2606.1Ų
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 1373.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)