FAIRMol

Z19456272

Pose ID 3135 Compound 100 Pose 425

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 Z19456272
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
16.5 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.17
Burial
82%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.931 kcal/mol/HA) ✓ Good fit quality (FQ -9.07) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Moderate strain (16.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-28.860
kcal/mol
LE
-0.931
kcal/mol/HA
Fit Quality
-9.07
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
16.5 kcal/mol
SASA buried
82%
Lipo contact
66% BSA apolar/total
SASA unbound
662 Ų
Apolar buried
356 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 5

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
Final rank4.485Score-28.860
Inter norm-0.990Intra norm0.059
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; 3 cofactor-context clashes
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 SER111 SER112 TYR114 TYR194 VAL230 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 overlap11Native recall0.65
Jaccard0.58RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue2HB residue recall0.40

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
458 0.27097943228209714 -0.811185 -19.6635 2 14 13 0.76 0.17 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 0 0.00 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 0.00 - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 0 0.00 0.00 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 0 0.00 0.00 - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 0 0.00 0.00 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 0 0.00 0.00 - no Open
91 3.5725886357035477 -0.950541 -26.1853 11 15 0 0.00 0.00 - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 0 0.00 0.00 - no Open
425 4.484716716621432 -0.989791 -28.8598 6 13 11 0.65 0.17 - 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 -28.860kcal/mol
Ligand efficiency (LE) -0.9310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.070
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 23.41kcal/mol
Minimised FF energy 6.91kcal/mol

SASA & burial

✓ computed
SASA (unbound) 662.5Ų
Total solvent-accessible surface area of free ligand
BSA total 542.2Ų
Buried surface area upon binding
BSA apolar 355.5Ų
Hydrophobic contacts buried
BSA polar 186.7Ų
Polar contacts buried
Fraction buried 81.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1591.0Ų
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 1016.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)