FAIRMol

Z56838410

Pose ID 9425 Compound 2071 Pose 617

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 Z56838410
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
26.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.38, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
62%
Reason: no major geometry red flags detected
2 protein-contact clashes 67% of hydrophobic surface is solvent-exposed (12/18 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 (-0.830 kcal/mol/HA) ✓ Good fit quality (FQ -7.64) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ High strain energy (26.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-21.573
kcal/mol
LE
-0.830
kcal/mol/HA
Fit Quality
-7.64
FQ (Leeson)
HAC
26
heavy atoms
MW
405
Da
LogP
4.07
cLogP
Strain ΔE
26.1 kcal/mol
SASA buried
76%
Lipo contact
62% BSA apolar/total
SASA unbound
631 Ų
Apolar buried
300 Ų

Interaction summary

HB 8 HY 2 PI 0 CLASH 2 ⚠ Exposure 66%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (12/18 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 18 Buried (contacted) 6 Exposed 12 LogP 4.07 H-bonds 8
Exposed fragments: phenyl (3/5 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
Final rank1.948Score-21.573
Inter norm-0.885Intra norm0.056
Top1000noExcludedno
Contacts14H-bonds8
Artifact reasongeometry warning; 5 clashes; 1 protein clash; moderate strain Δ 26.1
Residues
ARG242 ARG337 ARG50 ASP243 ASP385 ASP47 GLU384 LEU339 LYS51 MET386 PHE383 SER282 THR241 VAL336

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
Jaccard0.38RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.40

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
613 -0.18740807024469855 -0.988078 -24.4022 1 19 0 0.00 0.00 - no Open
613 1.6514746782569736 -1.12256 -24.7464 5 15 0 0.00 0.00 - no Open
617 1.948115621628624 -0.885262 -21.5725 8 14 8 0.53 0.20 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -21.573kcal/mol
Ligand efficiency (LE) -0.8297kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.644
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 404.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.07
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -2.24kcal/mol
Minimised FF energy -28.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 630.9Ų
Total solvent-accessible surface area of free ligand
BSA total 479.6Ų
Buried surface area upon binding
BSA apolar 299.9Ų
Hydrophobic contacts buried
BSA polar 179.7Ų
Polar contacts buried
Fraction buried 76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2388.3Ų
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 1376.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)