FAIRMol

MK155

Pose ID 9104 Compound 73 Pose 296

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand MK155
PDB1NJJ↗

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 mixed SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.20
Burial
65%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes 74% of hydrophobic surface is solvent-exposed (17/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.658 kcal/mol/HA) ✓ Good fit quality (FQ -6.35) ✓ Good H-bonds (3 bonds) ✓ Good burial (65% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Moderate strain (19.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-19.743
kcal/mol
LE
-0.658
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
30
heavy atoms
MW
410
Da
LogP
4.14
cLogP
Final rank
3.6098
rank score
Inter norm
-0.805
normalised
Contacts
12
H-bonds 6
Strain ΔE
19.0 kcal/mol
SASA buried
65%
Lipo contact
79% BSA apolar/total
SASA unbound
690 Ų
Apolar buried
352 Ų

Interaction summary

HBD 1 HBA 2 HY 1 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap8Native recall0.53
Jaccard0.42RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
327 0.8171546905266917 -0.881496 -24.9437 2 19 0 0.00 0.00 - no Open
252 1.25262528314132 -0.815055 -21.9899 5 19 0 0.00 0.00 - no Open
190 2.393610264960986 -1.01227 -27.9274 9 17 0 0.00 0.00 - no Open
274 2.6728153685243323 -0.971128 -26.73 9 17 0 0.00 0.00 - no Open
228 3.509170011564179 -0.852226 -22.326 3 16 0 0.00 0.00 - no Open
296 3.6097912474495737 -0.80505 -19.7428 6 12 8 0.53 0.20 - no Current
294 3.8954333947123394 -0.850379 -23.5994 8 19 0 0.00 0.00 - no Open
204 3.980686356420171 -1.15557 -33.8409 13 17 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 -19.743kcal/mol
Ligand efficiency (LE) -0.6581kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.348
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 410.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.14
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.37kcal/mol
Minimised FF energy 40.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 689.9Ų
Total solvent-accessible surface area of free ligand
BSA total 446.2Ų
Buried surface area upon binding
BSA apolar 352.2Ų
Hydrophobic contacts buried
BSA polar 93.9Ų
Polar contacts buried
Fraction buried 64.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2531.0Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1383.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)