FAIRMol

Z29582968

Pose ID 3297 Compound 2199 Pose 587

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
T05
L. major PTR1 L. major
Ligand Z29582968
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
28.8 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.59, Jaccard 0.50, H-bond role recall 0.50
Burial
76%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
2 protein-contact clashes 4 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (14/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.881 kcal/mol/HA) ✓ Good fit quality (FQ -8.95) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (28.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-31.709
kcal/mol
LE
-0.881
kcal/mol/HA
Fit Quality
-8.95
FQ (Leeson)
HAC
36
heavy atoms
MW
483
Da
LogP
3.79
cLogP
Strain ΔE
28.8 kcal/mol
SASA buried
76%
Lipo contact
82% BSA apolar/total
SASA unbound
796 Ų
Apolar buried
498 Ų

Interaction summary

HB 6 HY 16 PI 1 CLASH 4 ⚠ Exposure 50%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (14/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28 Buried (contacted) 14 Exposed 14 LogP 3.79 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.712Score-31.709
Inter norm-0.850Intra norm-0.031
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 15 clashes; 1 protein clash; 4 cofactor-context clashes; moderate strain Δ 28.7
Residues
ARG17 ARG39 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 SER111 SER112 TYR114 TYR194 ARG287

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
Jaccard0.50RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.60

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
587 2.7118252926811177 -0.850101 -31.709 6 13 10 0.59 0.50 - no Current
622 3.1966677246792456 -0.733856 -21.8263 2 20 0 0.00 0.00 - no Open
602 3.658774291326658 -0.594465 -20.3694 5 12 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 -31.709kcal/mol
Ligand efficiency (LE) -0.8808kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.952
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 482.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.79
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.02kcal/mol
Minimised FF energy 30.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 796.5Ų
Total solvent-accessible surface area of free ligand
BSA total 603.8Ų
Buried surface area upon binding
BSA apolar 497.9Ų
Hydrophobic contacts buried
BSA polar 105.9Ų
Polar contacts buried
Fraction buried 75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1773.5Ų
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 1086.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)