FAIRMol

ulfkktlib_1343

Pose ID 9007 Compound 4147 Pose 199

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 ulfkktlib_1343
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
16.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.30, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
1 protein-contact clashes 62% of hydrophobic surface is solvent-exposed (10/16 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 (-0.929 kcal/mol/HA) ✓ Good fit quality (FQ -8.07) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (16.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-20.439
kcal/mol
LE
-0.929
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
22
heavy atoms
MW
296
Da
LogP
0.99
cLogP
Strain ΔE
16.4 kcal/mol
SASA buried
83%
Lipo contact
89% BSA apolar/total
SASA unbound
560 Ų
Apolar buried
411 Ų

Interaction summary

HB 7 HY 8 PI 0 CLASH 1 ⚠ Exposure 62%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (10/16 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 16 Buried (contacted) 6 Exposed 10 LogP 0.99 H-bonds 7
Exposed fragments: phenyl (3/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank2.506Score-20.439
Inter norm-1.008Intra norm0.076
Top1000noExcludedno
Contacts15H-bonds7
Artifact reasongeometry warning; 8 clashes; 1 protein clash
Residues
ALA283 ARG22 ARG50 ASN20 ASP385 ASP44 ASP47 GLN341 GLU384 LEU25 LEU382 PHE284 SER282 THR21 THR285

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 overlap7Native recall0.47
Jaccard0.30RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
199 2.5064332962759415 -1.00755 -20.439 7 15 7 0.47 0.20 - no Current
145 4.036094008670908 -1.13717 -19.9707 12 9 0 0.00 0.00 - no Open
228 4.349187855054714 -0.847936 -18.7652 8 11 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 -20.439kcal/mol
Ligand efficiency (LE) -0.9290kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.066
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 296.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.99
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.61kcal/mol
Minimised FF energy 43.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 559.5Ų
Total solvent-accessible surface area of free ligand
BSA total 463.5Ų
Buried surface area upon binding
BSA apolar 410.7Ų
Hydrophobic contacts buried
BSA polar 52.9Ų
Polar contacts buried
Fraction buried 82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2457.7Ų
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 1389.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)