FAIRMol

Z237462396

Pose ID 9176 Compound 3802 Pose 368

DB SELECTIONDocking 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 Z237462396
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
27.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.20
Burial
74%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
2 protein-contact clashes 65% of hydrophobic surface is solvent-exposed (11/17 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 (-0.843 kcal/mol/HA) ✓ Good fit quality (FQ -7.55) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (27.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-20.222
kcal/mol
LE
-0.843
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
24
heavy atoms
MW
316
Da
LogP
2.46
cLogP
Strain ΔE
27.9 kcal/mol
SASA buried
74%
Lipo contact
72% BSA apolar/total
SASA unbound
556 Ų
Apolar buried
296 Ų

Interaction summary

HB 7 HY 2 PI 0 CLASH 2 ⚠ Exposure 64%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17 Buried (contacted) 6 Exposed 11 LogP 2.46 H-bonds 7
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (1/5 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.302Score-20.222
Inter norm-1.059Intra norm0.217
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 27.9
Residues
ARG242 ARG337 ASP243 ASP385 ASP47 GLU384 GLY240 LEU339 LYS51 PHE383 SER282 THR241 VAL336

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
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
Jaccard0.40RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.40

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
460 2.6128996786723255 -1.00729 -22.2601 6 13 0 0.00 0.00 - no Open
368 3.302336009876763 -1.05947 -20.2217 7 13 8 0.53 0.20 - no Current
359 3.7690631860668535 -0.996286 -22.0331 7 14 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 -20.222kcal/mol
Ligand efficiency (LE) -0.8426kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.551
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 316.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.46
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 81.95kcal/mol
Minimised FF energy 54.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 555.7Ų
Total solvent-accessible surface area of free ligand
BSA total 413.8Ų
Buried surface area upon binding
BSA apolar 295.8Ų
Hydrophobic contacts buried
BSA polar 118.0Ų
Polar contacts buried
Fraction buried 74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2367.6Ų
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 1392.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)