FAIRMol

ulfkktlib_3198

Pose ID 2919 Compound 1826 Pose 209

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
T05
L. major PTR1 L. major
Ligand ulfkktlib_3198
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
20.1 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.59, Jaccard 0.53, H-bond role recall 0.17
Burial
98%
Hydrophobic fit
61%
Reason: 9 internal clashes
9 intramolecular clashes 60% of hydrophobic surface is solvent-exposed (6/10 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 (-1.540 kcal/mol/HA) ✓ Good fit quality (FQ -12.62) ✓ Good H-bonds (5 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (61%) ✗ High strain energy (20.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.261
kcal/mol
LE
-1.540
kcal/mol/HA
Fit Quality
-12.62
FQ (Leeson)
HAC
19
heavy atoms
MW
274
Da
LogP
2.05
cLogP
Final rank
1.6237
rank score
Inter norm
-1.567
normalised
Contacts
12
H-bonds 6
Strain ΔE
20.1 kcal/mol
SASA buried
98%
Lipo contact
61% BSA apolar/total
SASA unbound
435 Ų
Apolar buried
261 Ų

Interaction summary

HBA 5 HY 4 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.59
Jaccard0.53RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.20

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
209 1.6236887881110724 -1.56692 -29.2607 6 12 10 0.59 0.17 - no Current
212 1.6243861870682983 -1.33802 -22.5434 6 9 9 0.53 0.50 - no Open
140 3.6213538173496707 -1.63035 -29.5306 10 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 -29.261kcal/mol
Ligand efficiency (LE) -1.5400kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.623
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 273.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.05
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 50.52kcal/mol
Minimised FF energy 30.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 435.5Ų
Total solvent-accessible surface area of free ligand
BSA total 424.4Ų
Buried surface area upon binding
BSA apolar 260.8Ų
Hydrophobic contacts buried
BSA polar 163.6Ų
Polar contacts buried
Fraction buried 97.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1428.5Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1022.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)