FAIRMol

Z728800606

Pose ID 9268 Compound 927 Pose 460

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 Z728800606
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 medium Native mixed SASA done
Strain ΔE
39.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.44, H-bond role recall 0.40
Burial
72%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 91% of hydrophobic surface is solvent-exposed (20/22 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 (-0.718 kcal/mol/HA) ✓ Good fit quality (FQ -7.12) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Very high strain energy (39.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-23.691
kcal/mol
LE
-0.718
kcal/mol/HA
Fit Quality
-7.12
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
-1.24
cLogP
Strain ΔE
39.3 kcal/mol
SASA buried
72%
Lipo contact
63% BSA apolar/total
SASA unbound
627 Ų
Apolar buried
285 Ų

Interaction summary

HB 9 HY 2 PI 0 CLASH 3 ⚠ Exposure 90%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
91% of hydrophobic surface is solvent-exposed (20/22 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 22 Buried (contacted) 2 Exposed 20 LogP -1.24 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank4.455Score-23.691
Inter norm-0.715Intra norm-0.002
Top1000noExcludedno
Contacts11H-bonds9
Artifact reasongeometry warning; 16 clashes; 2 protein clashes; high strain Δ 39.3
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 SER282 THR241 VAL335 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
Jaccard0.44RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
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
502 2.3986665171248642 -0.80522 -32.2604 3 18 0 0.00 0.00 - no Open
460 4.455243538874609 -0.715453 -23.6909 9 11 8 0.53 0.40 - no Current
441 6.264537143761146 -0.772484 -21.1602 16 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 -23.691kcal/mol
Ligand efficiency (LE) -0.7179kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.123
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 460.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.24
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 114.80kcal/mol
Minimised FF energy 75.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 626.9Ų
Total solvent-accessible surface area of free ligand
BSA total 454.1Ų
Buried surface area upon binding
BSA apolar 284.6Ų
Hydrophobic contacts buried
BSA polar 169.5Ų
Polar contacts buried
Fraction buried 72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2392.2Ų
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 1386.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)