FAIRMol

Z234853480

Pose ID 9290 Compound 2652 Pose 482

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 Z234853480
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
10.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.41, H-bond role recall 0.20
Burial
72%
Hydrophobic fit
59%
Reason: no major geometry red flags detected
1 protein-contact clashes 100% of hydrophobic surface is solvent-exposed (11/11 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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.355 kcal/mol/HA) ✓ Good fit quality (FQ -10.31) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (72% SASA buried) ✗ Moderate strain (10.6 kcal/mol) ✗ Geometry warnings
Score
-21.674
kcal/mol
LE
-1.355
kcal/mol/HA
Fit Quality
-10.31
FQ (Leeson)
HAC
16
heavy atoms
MW
234
Da
LogP
2.07
cLogP
Strain ΔE
10.6 kcal/mol
SASA buried
72%
Lipo contact
59% BSA apolar/total
SASA unbound
426 Ų
Apolar buried
182 Ų

Interaction summary

HB 6 HY 0 PI 0 CLASH 1 ⚠ Exposure 100%

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
No hy · hydrophobic contacts detected for this pose.

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (11/11 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 11 Buried (contacted) 0 Exposed 11 LogP 2.07 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (3/5 atoms exposed)
Final rank1.145Score-21.674
Inter norm-1.418Intra norm0.063
Top1000noExcludedno
Contacts9H-bonds6
Artifact reasongeometry warning; 3 clashes; 1 protein clash
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 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 overlap7Native recall0.47
Jaccard0.41RMSD-
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
451 -1.5078063148624512 -1.89844 -28.5321 6 11 0 0.00 0.00 - no Open
482 0.9816984890533861 -1.65262 -24.0361 8 15 0 0.00 0.00 - no Open
482 1.1445978680261857 -1.41808 -21.6735 6 9 7 0.47 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 -21.674kcal/mol
Ligand efficiency (LE) -1.3546kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.311
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 16HA

Physicochemical properties
Molecular weight 234.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 27.50kcal/mol
Minimised FF energy 16.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 425.9Ų
Total solvent-accessible surface area of free ligand
BSA total 308.3Ų
Buried surface area upon binding
BSA apolar 181.6Ų
Hydrophobic contacts buried
BSA polar 126.6Ų
Polar contacts buried
Fraction buried 72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2266.2Ų
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 1380.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)